chr7-25906050-G-A

Variant names:

• chr7-25906050-G-A
• rs7810044

Variant summary

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

The variant allele was found at a frequency of 0.364 in 152,092 control chromosomes in the GnomAD database, including 10,406 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 0.36 (10406 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.382
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.54 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

Frequencies

GnomAD3 genomes AF: 0.364 AC: 55338 AN: 151974 Hom.: 10404 Cov.: 32

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.380

Gnomad AMR AF: 0.285

Gnomad ASJ AF: 0.430

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.553

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.358

Gnomad NFE AF: 0.360

Gnomad OTH AF: 0.346

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

GnomAD4 genome AF: 0.364 AC: 55379 AN: 152092 Hom.: 10406 Cov.: 32 AF XY: 0.364 AC XY: 27039 AN XY: 74336

African (AFR) AF: 0.361 AC: 14962 AN: 41474

American (AMR) AF: 0.285 AC: 4355 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.430 AC: 1492 AN: 3468

East Asian (EAS) AF: 0.557 AC: 2877 AN: 5166

South Asian (SAS) AF: 0.554 AC: 2664 AN: 4812

European-Finnish (FIN) AF: 0.320 AC: 3382 AN: 10578

Middle Eastern (MID) AF: 0.354 AC: 104 AN: 294

European-Non Finnish (NFE) AF: 0.360 AC: 24461 AN: 67986

Other (OTH) AF: 0.348 AC: 735 AN: 2110

Alfa AF: 0.275 Hom.: 1102

Bravo AF: 0.359

Asia WGS AF: 0.534 AC: 1854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.4
DANN	Benign	0.73
PhyloP100		0.38

Splicing

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

Other links and lift over

dbSNP: rs7810044; hg19: chr7-25945670;