7-57088031-A-G

Position:

• chr7-57088031-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 0.572 in 151,340 control chromosomes in the GnomAD database, including 25,039 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 0.57 (25039 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.665 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.572 AC: 86515 AN: 151226 Hom.: 25016 Cov.: 32

Gnomad AFR AF: 0.594

Gnomad AMI AF: 0.575

Gnomad AMR AF: 0.597

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.683

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.524

Gnomad MID AF: 0.449

Gnomad NFE AF: 0.564

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.572 AC: 86589 AN: 151340 Hom.: 25039 Cov.: 32 AF XY: 0.571 AC XY: 42253 AN XY: 74008

Gnomad4 AFR AF: 0.595

Gnomad4 AMR AF: 0.598

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.684

Gnomad4 SAS AF: 0.525

Gnomad4 FIN AF: 0.524

Gnomad4 NFE AF: 0.564

Gnomad4 OTH AF: 0.543

Alfa AF: 0.560 Hom.: 3683

Bravo AF: 0.579

Asia WGS AF: 0.550 AC: 1914 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	14
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9719399; hg19: chr7-57155738;