rs7791702

Variant names:

• chr7-25483647-G-A
• rs7791702
• ENST00000650415.1:n.199+1731G>A

Variant summary

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

The ENST00000650415.1(ENSG00000285960):​n.199+1731G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.351 in 152,046 control chromosomes in the GnomAD database, including 9,542 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 0.35 (9542 hom., cov: 32)
• Consequence: ENSG00000285960 ENST00000650415.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.220
• Publications: 1 publications found

Genes affected

ENSG00000285960 (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 = 0.364 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
ENSG00000285960	ENST00000650415.1	n.199+1731G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.351 AC: 53372 AN: 151928 Hom.: 9531 Cov.: 32

Gnomad AFR AF: 0.356

Gnomad AMI AF: 0.279

Gnomad AMR AF: 0.315

Gnomad ASJ AF: 0.394

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.373

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.368

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.351 AC: 53410 AN: 152046 Hom.: 9542 Cov.: 32 AF XY: 0.348 AC XY: 25830 AN XY: 74316

African (AFR) AF: 0.356 AC: 14776 AN: 41464

American (AMR) AF: 0.314 AC: 4795 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.394 AC: 1366 AN: 3470

East Asian (EAS) AF: 0.214 AC: 1104 AN: 5170

South Asian (SAS) AF: 0.269 AC: 1297 AN: 4816

European-Finnish (FIN) AF: 0.373 AC: 3935 AN: 10560

Middle Eastern (MID) AF: 0.425 AC: 124 AN: 292

European-Non Finnish (NFE) AF: 0.368 AC: 25010 AN: 67984

Other (OTH) AF: 0.356 AC: 749 AN: 2106

Alfa AF: 0.361 Hom.: 3917

Bravo AF: 0.347

Asia WGS AF: 0.306 AC: 1063 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.3
DANN	Benign	0.72
PhyloP100		0.22

Splicing

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

Other links and lift over

dbSNP: rs7791702; hg19: chr7-25523266;