chr7-22757124-A-G

Variant names:

• chr7-22757124-A-G
• rs6461667

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 0.724 in 152,068 control chromosomes in the GnomAD database, including 42,000 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 0.72 (42000 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0640
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 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: 0.724 AC: 110031 AN: 151950 Hom.: 41933 Cov.: 31

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.615

Gnomad AMR AF: 0.798

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.840

Gnomad FIN AF: 0.476

Gnomad MID AF: 0.810

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.746

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

GnomAD4 genome AF: 0.724 AC: 110156 AN: 152068 Hom.: 42000 Cov.: 31 AF XY: 0.726 AC XY: 53930 AN XY: 74330

African (AFR) AF: 0.925 AC: 38408 AN: 41516

American (AMR) AF: 0.798 AC: 12198 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.763 AC: 2646 AN: 3466

East Asian (EAS) AF: 0.998 AC: 5171 AN: 5180

South Asian (SAS) AF: 0.839 AC: 4036 AN: 4808

European-Finnish (FIN) AF: 0.476 AC: 5026 AN: 10552

Middle Eastern (MID) AF: 0.810 AC: 238 AN: 294

European-Non Finnish (NFE) AF: 0.593 AC: 40291 AN: 67944

Other (OTH) AF: 0.748 AC: 1582 AN: 2114

Alfa AF: 0.609 Hom.: 12972

Bravo AF: 0.759

Asia WGS AF: 0.917 AC: 3184 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.7
DANN	Benign	0.30
PhyloP100		-0.064

Splicing

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

Other links and lift over

dbSNP: rs6461667; hg19: chr7-22796743;