7-57088031-A-G

Variant names:

• chr7-57088031-A-G
• rs9719399

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 0.572 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.595 AC: 24274 AN: 40826

American (AMR) AF: 0.598 AC: 9113 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1502 AN: 3470

East Asian (EAS) AF: 0.684 AC: 3527 AN: 5160

South Asian (SAS) AF: 0.525 AC: 2535 AN: 4824

European-Finnish (FIN) AF: 0.524 AC: 5521 AN: 10546

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.564 AC: 38321 AN: 67964

Other (OTH) AF: 0.543 AC: 1144 AN: 2106

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
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs9719399; hg19: chr7-57155738;