7-57088031-A-G

Variant names:

• chr7-57088031-A-G
• rs9719399

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 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

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;