rs1499646

Variant names:

• chr8-74155877-C-T
• rs1499646
• ENST00000668834.2:n.194-10148C>T

Variant summary

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

The ENST00000668834.2(ENSG00000254288):​n.194-10148C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.761 in 151,956 control chromosomes in the GnomAD database, including 44,777 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 0.76 (44777 hom., cov: 30)
• Consequence: ENSG00000254288 ENST00000668834.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.678
• Publications: 3 publications found

Genes affected

ENSG00000254288 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.77).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.902 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
ENSG00000254288	ENST00000668834.2	n.194-10148C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.762 AC: 115638 AN: 151838 Hom.: 44765 Cov.: 30

Gnomad AFR AF: 0.619

Gnomad AMI AF: 0.732

Gnomad AMR AF: 0.822

Gnomad ASJ AF: 0.802

Gnomad EAS AF: 0.924

Gnomad SAS AF: 0.735

Gnomad FIN AF: 0.821

Gnomad MID AF: 0.837

Gnomad NFE AF: 0.812

Gnomad OTH AF: 0.792

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

GnomAD4 genome AF: 0.761 AC: 115700 AN: 151956 Hom.: 44777 Cov.: 30 AF XY: 0.762 AC XY: 56627 AN XY: 74282

African (AFR) AF: 0.619 AC: 25619 AN: 41396

American (AMR) AF: 0.821 AC: 12550 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.802 AC: 2780 AN: 3468

East Asian (EAS) AF: 0.924 AC: 4774 AN: 5166

South Asian (SAS) AF: 0.735 AC: 3536 AN: 4814

European-Finnish (FIN) AF: 0.821 AC: 8670 AN: 10554

Middle Eastern (MID) AF: 0.831 AC: 241 AN: 290

European-Non Finnish (NFE) AF: 0.812 AC: 55194 AN: 67968

Other (OTH) AF: 0.791 AC: 1668 AN: 2110

Alfa AF: 0.794 Hom.: 26504

Bravo AF: 0.758

Asia WGS AF: 0.806 AC: 2799 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	14
DANN	Benign	0.88
PhyloP100		0.68

Splicing

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

Other links and lift over

dbSNP: rs1499646; hg19: chr8-75068112;