13-37611253-G-A

Variant names:

• chr13-37611253-G-A
• rs7992705
• ENST00000744989.1:n.48+14216G>A

Variant summary

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

The ENST00000744989.1(ENSG00000297050):​n.48+14216G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.294 in 152,070 control chromosomes in the GnomAD database, including 7,028 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 0.29 (7028 hom., cov: 32)
• Consequence: ENSG00000297050 ENST00000744989.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.128
• Publications: 1 publications found

Genes affected

ENSG00000297050 (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 = 0.348 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000744989.1. 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
	ENSG00000297050	ENST00000744989.1		n.48+14216G>A		intron	N/A
	ENSG00000297050	ENST00000744990.1		n.70+14216G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.294 AC: 44737 AN: 151952 Hom.: 7018 Cov.: 32

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.272

Gnomad AMR AF: 0.291

Gnomad ASJ AF: 0.493

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.336

Gnomad FIN AF: 0.254

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.352

Gnomad OTH AF: 0.311

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

GnomAD4 genome AF: 0.294 AC: 44764 AN: 152070 Hom.: 7028 Cov.: 32 AF XY: 0.286 AC XY: 21230 AN XY: 74338

African (AFR) AF: 0.206 AC: 8560 AN: 41482

American (AMR) AF: 0.291 AC: 4447 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.493 AC: 1711 AN: 3468

East Asian (EAS) AF: 0.161 AC: 829 AN: 5162

South Asian (SAS) AF: 0.336 AC: 1619 AN: 4820

European-Finnish (FIN) AF: 0.254 AC: 2686 AN: 10586

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.352 AC: 23918 AN: 67958

Other (OTH) AF: 0.314 AC: 661 AN: 2108

Alfa AF: 0.187 Hom.: 411

Bravo AF: 0.295

Asia WGS AF: 0.257 AC: 894 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.55
PhyloP100		-0.13

Splicing

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

Other links and lift over

dbSNP: rs7992705; hg19: chr13-38185390; COSMIC: COSV69347293;