chr7-25910925-A-C

Variant names:

• chr7-25910925-A-C
• rs10261878

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 0.804 in 152,020 control chromosomes in the GnomAD database, including 52,899 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 0.80 (52899 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.875
• Publications: 22 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.939 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: 0.804 AC: 122161 AN: 151902 Hom.: 52884 Cov.: 31

Gnomad AFR AF: 0.445

Gnomad AMI AF: 0.995

Gnomad AMR AF: 0.893

Gnomad ASJ AF: 0.911

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.950

Gnomad FIN AF: 0.970

Gnomad MID AF: 0.862

Gnomad NFE AF: 0.945

Gnomad OTH AF: 0.839

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

GnomAD4 genome AF: 0.804 AC: 122220 AN: 152020 Hom.: 52899 Cov.: 31 AF XY: 0.810 AC XY: 60213 AN XY: 74346

African (AFR) AF: 0.445 AC: 18444 AN: 41410

American (AMR) AF: 0.894 AC: 13649 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.911 AC: 3162 AN: 3470

East Asian (EAS) AF: 0.959 AC: 4973 AN: 5186

South Asian (SAS) AF: 0.950 AC: 4566 AN: 4808

European-Finnish (FIN) AF: 0.970 AC: 10260 AN: 10578

Middle Eastern (MID) AF: 0.862 AC: 250 AN: 290

European-Non Finnish (NFE) AF: 0.945 AC: 64241 AN: 67988

Other (OTH) AF: 0.840 AC: 1768 AN: 2106

Alfa AF: 0.820 Hom.: 15332

Bravo AF: 0.780

Asia WGS AF: 0.918 AC: 3149 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.3
DANN	Benign	0.56
PhyloP100		-0.88

Splicing

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

Other links and lift over

dbSNP: rs10261878; hg19: chr7-25950545;