chr7-118031684-A-T

Variant names:

• chr7-118031684-A-T
• rs10487383

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 0.104 in 152,192 control chromosomes in the GnomAD database, including 2,049 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 0.10 (2049 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0730

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.357 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: 0.104 AC: 15740 AN: 152074 Hom.: 2047 Cov.: 33

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0651

Gnomad ASJ AF: 0.0138

Gnomad EAS AF: 0.371

Gnomad SAS AF: 0.0671

Gnomad FIN AF: 0.00989

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0107

Gnomad OTH AF: 0.0898

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

GnomAD4 genome AF: 0.104 AC: 15763 AN: 152192 Hom.: 2049 Cov.: 33 AF XY: 0.103 AC XY: 7637 AN XY: 74396

Gnomad4 AFR AF: 0.276

Gnomad4 AMR AF: 0.0653

Gnomad4 ASJ AF: 0.0138

Gnomad4 EAS AF: 0.371

Gnomad4 SAS AF: 0.0671

Gnomad4 FIN AF: 0.00989

Gnomad4 NFE AF: 0.0107

Gnomad4 OTH AF: 0.0907

Alfa AF: 0.0601 Hom.: 122

Bravo AF: 0.118

Asia WGS AF: 0.205 AC: 710 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	4.7
DANN	Benign	0.86

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487383; hg19: chr7-117671738;