rs7992626

Variant names:

• chr13-67841275-C-T
• rs7992626
• ENST00000775040.1:n.102+16697G>A

Variant summary

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

The ENST00000775040.1(ENSG00000300912):​n.102+16697G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,096 control chromosomes in the GnomAD database, including 2,640 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 0.18 (2640 hom., cov: 32)
• Consequence: ENSG00000300912 ENST00000775040.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 0 publications found

Genes affected

ENSG00000300912 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.224 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775040.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000300912	ENST00000775040.1		n.102+16697G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27802 AN: 151976 Hom.: 2622 Cov.: 32

Gnomad AFR AF: 0.181

Gnomad AMI AF: 0.103

Gnomad AMR AF: 0.196

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.235

Gnomad FIN AF: 0.122

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.191

Gnomad OTH AF: 0.212

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

GnomAD4 genome AF: 0.183 AC: 27868 AN: 152096 Hom.: 2640 Cov.: 32 AF XY: 0.181 AC XY: 13427 AN XY: 74332

African (AFR) AF: 0.181 AC: 7522 AN: 41488

American (AMR) AF: 0.197 AC: 3007 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.197 AC: 682 AN: 3468

East Asian (EAS) AF: 0.118 AC: 606 AN: 5156

South Asian (SAS) AF: 0.236 AC: 1135 AN: 4814

European-Finnish (FIN) AF: 0.122 AC: 1288 AN: 10572

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.191 AC: 13005 AN: 67988

Other (OTH) AF: 0.216 AC: 458 AN: 2116

Alfa AF: 0.189 Hom.: 1125

Bravo AF: 0.188

Asia WGS AF: 0.208 AC: 720 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.7
DANN	Benign	0.67
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs7992626; hg19: chr13-68415407; COSMIC: COSV68422071;