dbSNP rs17664587: ENSG00000249169:n.89+6056C>T (chr5-92660992-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2

The ENST00000512237.1(ENSG00000249169):n.89+6056C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0352 in 151,670 control chromosomes in the GnomAD database, including 119 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.035 ( 119 hom., cov: 32)

Exomes 𝑓: 0.028 ( 0 hom. )

Consequence

ENSG00000249169
ENST00000512237.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.651

Variant links:

Genes affected

ENSG00000249169 (HGNC:):

ENSG00000249169 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.99).

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0352 (5344/151634) while in subpopulation NFE AF= 0.0495 (3349/67656). AF 95% confidence interval is 0.0481. There are 119 homozygotes in gnomad4. There are 2493 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 119 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105379082	NR_188296.1 link	n.362+8760G>A	intron_variant	Intron 3 of 3
LOC105379082	NR_188297.1 link	n.217+10492G>A	intron_variant	Intron 2 of 2
LOC105379082	NR_188298.1 link	n.217+10492G>A	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000249169	ENST00000512237.1 link	n.89+6056C>T		intron_variant	Intron 1 of 1	3
ENSG00000249776	ENST00000513779.1 link	n.-129G>A		upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.0353

AC:

5346

AN:

151516

Hom.:

119

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0144

Gnomad AMI

AF:

0.0439

Gnomad AMR

AF:

0.0407

Gnomad ASJ

AF:

0.0560

Gnomad EAS

AF:

0.000389

Gnomad SAS

AF:

0.0315

Gnomad FIN

AF:

0.0278

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0495

Gnomad OTH

AF:

0.0374

GnomAD4 exome

AF:

0.0278

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.0278

GnomAD4 genome

AF:

0.0352

AC:

5344

AN:

151634

Hom.:

119

Cov.:

AF XY:

0.0337

AC XY:

2493

AN XY:

74080

show subpopulations

Gnomad4 AFR

AF:

0.0144

Gnomad4 AMR

AF:

0.0407

Gnomad4 ASJ

AF:

0.0560

Gnomad4 EAS

AF:

0.000390

Gnomad4 SAS

AF:

0.0315

Gnomad4 FIN

AF:

0.0278

Gnomad4 NFE

AF:

0.0495

Gnomad4 OTH

AF:

0.0366

Alfa

AF:

0.0471

Hom.:

246

Bravo

AF:

0.0357

Asia WGS

AF:

0.0120

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

4.5

DANN

Benign

0.56

Splicing

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over