7-22741526-G-A

Variant names:

• chr7-22741526-G-A
• rs2177473

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 0.417 in 152,038 control chromosomes in the GnomAD database, including 15,168 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 0.42 (15168 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.249
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.892 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: 0.417 AC: 63360 AN: 151920 Hom.: 15127 Cov.: 32

Gnomad AFR AF: 0.545

Gnomad AMI AF: 0.391

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.913

Gnomad SAS AF: 0.631

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.417 AC: 63463 AN: 152038 Hom.: 15168 Cov.: 32 AF XY: 0.422 AC XY: 31390 AN XY: 74318

African (AFR) AF: 0.546 AC: 22616 AN: 41446

American (AMR) AF: 0.468 AC: 7149 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3470

East Asian (EAS) AF: 0.913 AC: 4731 AN: 5180

South Asian (SAS) AF: 0.631 AC: 3035 AN: 4810

European-Finnish (FIN) AF: 0.228 AC: 2414 AN: 10582

Middle Eastern (MID) AF: 0.650 AC: 191 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20178 AN: 67944

Other (OTH) AF: 0.474 AC: 1003 AN: 2116

Alfa AF: 0.202 Hom.: 479

Bravo AF: 0.442

Asia WGS AF: 0.756 AC: 2625 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
CADD	Benign	4.8
DANN	Benign	0.84
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs2177473; hg19: chr7-22781145;