7-22758461-T-C

Variant names:

• chr7-22758461-T-C
• rs7808122

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 0.639 in 151,962 control chromosomes in the GnomAD database, including 32,012 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 0.64 (32012 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.272
• Publications: 18 publications found

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 (EAS) allele frequency at 95% confidence interval = 0.97 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.639 AC: 96973 AN: 151844 Hom.: 31970 Cov.: 31

Gnomad AFR AF: 0.716

Gnomad AMI AF: 0.610

Gnomad AMR AF: 0.735

Gnomad ASJ AF: 0.689

Gnomad EAS AF: 0.993

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.446

Gnomad MID AF: 0.763

Gnomad NFE AF: 0.559

Gnomad OTH AF: 0.675

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

GnomAD4 genome AF: 0.639 AC: 97068 AN: 151962 Hom.: 32012 Cov.: 31 AF XY: 0.642 AC XY: 47650 AN XY: 74264

African (AFR) AF: 0.716 AC: 29679 AN: 41454

American (AMR) AF: 0.735 AC: 11228 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.689 AC: 2392 AN: 3470

East Asian (EAS) AF: 0.993 AC: 5138 AN: 5174

South Asian (SAS) AF: 0.783 AC: 3769 AN: 4816

European-Finnish (FIN) AF: 0.446 AC: 4688 AN: 10512

Middle Eastern (MID) AF: 0.755 AC: 222 AN: 294

European-Non Finnish (NFE) AF: 0.559 AC: 37966 AN: 67948

Other (OTH) AF: 0.679 AC: 1432 AN: 2108

Alfa AF: 0.599 Hom.: 78212

Bravo AF: 0.663

Asia WGS AF: 0.874 AC: 3034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.5
DANN	Benign	0.64
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs7808122; hg19: chr7-22798080;