rs958660

Variant names:

• chr8-2212161-G-A
• rs958660
• ENST00000776947.1:n.212+8611G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000776947.1(ENSG00000288782):​n.212+8611G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.063 in 151,852 control chromosomes in the GnomAD database, including 504 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 0.063 (504 hom., cov: 32)
• Consequence: ENSG00000288782 ENST00000776947.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.581
• Publications: 0 publications found

Genes affected

ENSG00000288782 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0973 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288782	ENST00000776947.1	n.212+8611G>A		intron_variant	Intron 1 of 2
ENSG00000301228	ENST00000777202.1	n.257+3639C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0631 AC: 9567 AN: 151734 Hom.: 503 Cov.: 32

Gnomad AFR AF: 0.0185

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.0542

Gnomad ASJ AF: 0.0728

Gnomad EAS AF: 0.000585

Gnomad SAS AF: 0.0472

Gnomad FIN AF: 0.0411

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0993

Gnomad OTH AF: 0.0728

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0630 AC: 9569 AN: 151852 Hom.: 504 Cov.: 32 AF XY: 0.0593 AC XY: 4398 AN XY: 74134

African (AFR) AF: 0.0184 AC: 764 AN: 41506

American (AMR) AF: 0.0542 AC: 828 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0728 AC: 251 AN: 3448

East Asian (EAS) AF: 0.000586 AC: 3 AN: 5118

South Asian (SAS) AF: 0.0479 AC: 229 AN: 4782

European-Finnish (FIN) AF: 0.0411 AC: 429 AN: 10450

Middle Eastern (MID) AF: 0.0816 AC: 24 AN: 294

European-Non Finnish (NFE) AF: 0.0993 AC: 6745 AN: 67948

Other (OTH) AF: 0.0725 AC: 153 AN: 2110

Alfa AF: 0.0763 Hom.: 90

Bravo AF: 0.0628

Asia WGS AF: 0.0270 AC: 95 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.1
DANN	Benign	0.59
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs958660; hg19: chr8-2159828;