chr7-57269594-A-G

Variant names:

• chr7-57269594-A-G
• rs6942880

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 0.387 in 152,082 control chromosomes in the GnomAD database, including 11,798 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 0.39 (11798 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.91
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.08).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.449 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: 0.387 AC: 58881 AN: 151964 Hom.: 11801 Cov.: 32

Gnomad AFR AF: 0.317

Gnomad AMI AF: 0.451

Gnomad AMR AF: 0.354

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.296

Gnomad SAS AF: 0.395

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.453

Gnomad OTH AF: 0.392

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

GnomAD4 genome AF: 0.387 AC: 58908 AN: 152082 Hom.: 11798 Cov.: 32 AF XY: 0.380 AC XY: 28263 AN XY: 74324

African (AFR) AF: 0.317 AC: 13142 AN: 41500

American (AMR) AF: 0.353 AC: 5402 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1410 AN: 3472

East Asian (EAS) AF: 0.295 AC: 1526 AN: 5168

South Asian (SAS) AF: 0.395 AC: 1902 AN: 4816

European-Finnish (FIN) AF: 0.320 AC: 3380 AN: 10568

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.453 AC: 30774 AN: 67958

Other (OTH) AF: 0.393 AC: 830 AN: 2112

Alfa AF: 0.401 Hom.: 1515

Bravo AF: 0.383

Asia WGS AF: 0.371 AC: 1294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.47
DANN	Benign	0.30
PhyloP100		-2.9

Splicing

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

Other links and lift over

dbSNP: rs6942880; hg19: chr7-57337301;