7-839130-T-C

Position:

• chr7-839130-T-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate BA1

The NM_001130965.3(SUN1):​c.266+144T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.768 in 711,780 control chromosomes in the GnomAD database, including 210,662 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.78 (46045 hom., cov: 34)
  • Exomes 𝑓: 0.77 (164617 hom.)
• Consequence: SUN1 NM_001130965.3 intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -0.0850

Genes affected

SUN1 (HGNC:18587): (Sad1 and UNC84 domain containing 1) This gene is a member of the unc-84 homolog family and encodes a nuclear envelope protein with an Unc84 (SUN) domain. The protein is involved in nuclear anchorage and migration. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jan 2019]

ACMG classification

Verdict is Benign. Variant got -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BP6: Variant 7-839130-T-C is Benign according to our data. Variant chr7-839130-T-C is described in ClinVar as [Benign]. Clinvar id is 1253189.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.818 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SUN1	NM_001130965.3	c.266+144T>C		intron_variant		ENST00000401592.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SUN1	ENST00000401592.6	c.266+144T>C		intron_variant		1	NM_001130965.3	P3

Frequencies

GnomAD3 genomes AF: 0.776 AC: 118133 AN: 152146 Hom.: 45990 Cov.: 34

Gnomad AFR AF: 0.754

Gnomad AMI AF: 0.822

Gnomad AMR AF: 0.830

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.807

Gnomad SAS AF: 0.764

Gnomad FIN AF: 0.878

Gnomad MID AF: 0.703

Gnomad NFE AF: 0.765

Gnomad OTH AF: 0.753

GnomAD4 exome AF: 0.766 AC: 428324 AN: 559516 Hom.: 164617 Cov.: 8 AF XY: 0.766 AC XY: 214192 AN XY: 279802

Gnomad4 AFR exome AF: 0.750

Gnomad4 AMR exome AF: 0.851

Gnomad4 ASJ exome AF: 0.718

Gnomad4 EAS exome AF: 0.795

Gnomad4 SAS exome AF: 0.739

Gnomad4 FIN exome AF: 0.866

Gnomad4 NFE exome AF: 0.759

Gnomad4 OTH exome AF: 0.766

GnomAD4 genome AF: 0.777 AC: 118249 AN: 152264 Hom.: 46045 Cov.: 34 AF XY: 0.781 AC XY: 58158 AN XY: 74456

Gnomad4 AFR AF: 0.754

Gnomad4 AMR AF: 0.830

Gnomad4 ASJ AF: 0.706

Gnomad4 EAS AF: 0.807

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.878

Gnomad4 NFE AF: 0.765

Gnomad4 OTH AF: 0.755

Alfa AF: 0.768 Hom.: 5974

Bravo AF: 0.771

Asia WGS AF: 0.826 AC: 2873 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

GeneDx

May 15, 2021

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.1
DANN	Benign	0.43

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

Other links and lift over

dbSNP: rs1127460; hg19: chr7-878767;