7-25008626-T-C

Variant names:

• chr7-25008626-T-C
• rs167

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 0.849 in 152,114 control chromosomes in the GnomAD database, including 55,219 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 0.85 (55219 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.93 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: 0.849 AC: 129042 AN: 151996 Hom.: 55151 Cov.: 31

Gnomad AFR AF: 0.938

Gnomad AMI AF: 0.708

Gnomad AMR AF: 0.870

Gnomad ASJ AF: 0.803

Gnomad EAS AF: 0.836

Gnomad SAS AF: 0.932

Gnomad FIN AF: 0.768

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.802

Gnomad OTH AF: 0.854

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

GnomAD4 genome AF: 0.849 AC: 129170 AN: 152114 Hom.: 55219 Cov.: 31 AF XY: 0.851 AC XY: 63264 AN XY: 74338

African (AFR) AF: 0.938 AC: 38948 AN: 41536

American (AMR) AF: 0.871 AC: 13303 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.803 AC: 2787 AN: 3470

East Asian (EAS) AF: 0.836 AC: 4328 AN: 5176

South Asian (SAS) AF: 0.932 AC: 4496 AN: 4824

European-Finnish (FIN) AF: 0.768 AC: 8078 AN: 10520

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.802 AC: 54516 AN: 67992

Other (OTH) AF: 0.855 AC: 1805 AN: 2110

Alfa AF: 0.832 Hom.: 6428

Bravo AF: 0.857

Asia WGS AF: 0.890 AC: 3096 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.85
DANN	Benign	0.26
PhyloP100		-0.98

Splicing

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

Other links and lift over

dbSNP: rs167; hg19: chr7-25048245;