7-22771597-T-C

Variant names:

• chr7-22771597-T-C
• rs10244467

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 0.0984 in 152,192 control chromosomes in the GnomAD database, including 891 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 0.098 (891 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.14 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Frequencies

GnomAD3 genomes AF: 0.0984 AC: 14958 AN: 152074 Hom.: 893 Cov.: 31

Gnomad AFR AF: 0.143

Gnomad AMI AF: 0.0417

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.198

Gnomad EAS AF: 0.000770

Gnomad SAS AF: 0.0937

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.299

Gnomad NFE AF: 0.0763

Gnomad OTH AF: 0.118

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

GnomAD4 genome AF: 0.0984 AC: 14969 AN: 152192 Hom.: 891 Cov.: 31 AF XY: 0.0988 AC XY: 7351 AN XY: 74416

African (AFR) AF: 0.143 AC: 5924 AN: 41516

American (AMR) AF: 0.0826 AC: 1263 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.198 AC: 687 AN: 3472

East Asian (EAS) AF: 0.000772 AC: 4 AN: 5182

South Asian (SAS) AF: 0.0950 AC: 457 AN: 4808

European-Finnish (FIN) AF: 0.102 AC: 1075 AN: 10588

Middle Eastern (MID) AF: 0.284 AC: 83 AN: 292

European-Non Finnish (NFE) AF: 0.0764 AC: 5193 AN: 68010

Other (OTH) AF: 0.116 AC: 245 AN: 2114

Alfa AF: 0.0921 Hom.: 100

Bravo AF: 0.101

Asia WGS AF: 0.0430 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	9.0
DANN	Benign	0.86
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs10244467; hg19: chr7-22811216;