chr7-57269594-A-G

Position:

• chr7-57269594-A-G

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	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

Gnomad4 AFR AF: 0.317

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.406

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.395

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.453

Gnomad4 OTH AF: 0.393

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 v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6942880; hg19: chr7-57337301;