rs10487438

Positions:

• chr7-126208272-G-C

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 0.0874 in 152,044 control chromosomes in the GnomAD database, including 868 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 0.087 (868 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.143

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.181 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: 0.0873 AC: 13260 AN: 151926 Hom.: 865 Cov.: 32

Gnomad AFR AF: 0.184

Gnomad AMI AF: 0.0658

Gnomad AMR AF: 0.0492

Gnomad ASJ AF: 0.0447

Gnomad EAS AF: 0.0832

Gnomad SAS AF: 0.0442

Gnomad FIN AF: 0.113

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0386

Gnomad OTH AF: 0.0822

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

GnomAD4 genome AF: 0.0874 AC: 13288 AN: 152044 Hom.: 868 Cov.: 32 AF XY: 0.0896 AC XY: 6653 AN XY: 74290

Gnomad4 AFR AF: 0.185

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0447

Gnomad4 EAS AF: 0.0827

Gnomad4 SAS AF: 0.0442

Gnomad4 FIN AF: 0.113

Gnomad4 NFE AF: 0.0386

Gnomad4 OTH AF: 0.0818

Alfa AF: 0.0666 Hom.: 83

Bravo AF: 0.0884

Asia WGS AF: 0.0690 AC: 239 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.3
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10487438; hg19: chr7-125848326;