Genetic Variant SMC6:p.Ile491Leu (chr2-17716140-T-G) – ACMG Classification: Likely_benign (-5 pts)

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2

The NM_001142286.2(SMC6):c.1471A>C(p.Ile491Leu) variant causes a missense change. The variant allele was found at a frequency of 0.000011 in 1,458,102 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).

Frequency

Genomes: not found (cov: 32)

Exomes 𝑓: 0.000011 ( 0 hom. )

Consequence

SMC6
NM_001142286.2 missense

Scores

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 3.96

Variant links:

Genes affected

SMC6 (HGNC:20466): (structural maintenance of chromosomes 6) Enables ubiquitin protein ligase binding activity. Involved in several processes, including cellular senescence; positive regulation of chromosome segregation; and telomere maintenance via recombination. Located in chromosome and nuclear body. Part of Smc5-Smc6 complex. [provided by Alliance of Genome Resources, Apr 2022]

SMC6 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -5 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.34483594).

BS2

High AC in GnomAdExome4 at 16 AD gene.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SMC6	NM_001142286.2 link	c.1471A>C	p.Ile491Leu	missense_variant	Exon 15 of 28	ENST00000448223.7	NP_001135758.1	Q96SB8-1A0A2S1ZR87

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
SMC6	ENST00000448223.7 link	c.1471A>C	p.Ile491Leu	missense_variant	Exon 15 of 28	1	NM_001142286.2	ENSP00000404092.2	Q96SB8-1
SMC6	ENST00000351948.8 link	c.1471A>C	p.Ile491Leu	missense_variant	Exon 14 of 27	1		ENSP00000323439.4	Q96SB8-1
SMC6	ENST00000446852.5 link	c.1549A>C	p.Ile517Leu	missense_variant	Exon 16 of 20	1		ENSP00000408644.1	C9JMN1
SMC6	ENST00000402989.5 link	c.1471A>C	p.Ile491Leu	missense_variant	Exon 17 of 30	2		ENSP00000384539.1	Q96SB8-1

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.00000405

AC:

AN:

247216

Hom.:

AF XY:

0.00000747

AC XY:

AN XY:

133908

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.00000888

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.0000110

AC:

AN:

1458102

Hom.:

Cov.:

AF XY:

0.00000689

AC XY:

AN XY:

725486

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0000144

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Cov.:

Bravo

AF:

0.0000113

ExAC

AF:

0.00000824

AC:

EpiCase

AF:

0.00

EpiControl

AF:

0.0000596

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not specified

Uncertain:1

Jan 16, 2024

Ambry Genetics

Significance: Uncertain significance

Review Status: criteria provided, single submitter

Collection Method: clinical testing

The c.1471A>C (p.I491L) alteration is located in exon 15 (coding exon 13) of the SMC6 gene. This alteration results from a A to C substitution at nucleotide position 1471, causing the isoleucine (I) at amino acid position 491 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.26

BayesDel_addAF

Benign

-0.11

BayesDel_noAF

Benign

-0.40

CADD

Uncertain

DANN

Uncertain

0.99

DEOGEN2

Benign

0.10

T;T;T;.

Eigen

Uncertain

0.36

Eigen_PC

Uncertain

0.35

FATHMM_MKL

Uncertain

0.94

LIST_S2

Benign

0.80

.;.;T;T

M_CAP

Benign

0.019

MetaRNN

Benign

0.34

T;T;T;T

MetaSVM

Benign

-1.0

MutationAssessor

Uncertain

2.1

M;M;M;.

PrimateAI

Benign

0.44

PROVEAN

Benign

-1.8

N;N;N;N

REVEL

Benign

0.17

Sift

Benign

0.067

T;T;T;T

Sift4G

Benign

0.078

T;T;T;D

Polyphen

0.97

D;D;D;P

Vest4

0.47

MutPred

0.62

Loss of catalytic residue at I491 (P = 0.1863);Loss of catalytic residue at I491 (P = 0.1863);Loss of catalytic residue at I491 (P = 0.1863);.;

MVP

0.27

MPC

0.84

ClinPred

0.79

GERP RS

3.2

Varity_R

0.28

gMVP

0.80

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over