rs7914029

Positions:

• chr10-113250496-T-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 0.115 in 152,066 control chromosomes in the GnomAD database, including 1,673 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 0.12 (1673 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.866

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.261 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: 0.115 AC: 17456 AN: 151944 Hom.: 1661 Cov.: 30

Gnomad AFR AF: 0.264

Gnomad AMI AF: 0.0910

Gnomad AMR AF: 0.0618

Gnomad ASJ AF: 0.0752

Gnomad EAS AF: 0.0692

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.0470

Gnomad MID AF: 0.0886

Gnomad NFE AF: 0.0536

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.115 AC: 17507 AN: 152066 Hom.: 1673 Cov.: 30 AF XY: 0.112 AC XY: 8355 AN XY: 74332

Gnomad4 AFR AF: 0.265

Gnomad4 AMR AF: 0.0616

Gnomad4 ASJ AF: 0.0752

Gnomad4 EAS AF: 0.0691

Gnomad4 SAS AF: 0.102

Gnomad4 FIN AF: 0.0470

Gnomad4 NFE AF: 0.0536

Gnomad4 OTH AF: 0.103

Alfa AF: 0.0625 Hom.: 893

Bravo AF: 0.121

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.1
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7914029; hg19: chr10-115010255;