rs10934254

Positions:

• chr3-114122787-G-A

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 0.467 in 152,094 control chromosomes in the GnomAD database, including 18,258 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 0.47 (18258 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0600

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.575 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: 0.468 AC: 71053 AN: 151978 Hom.: 18260 Cov.: 32

Gnomad AFR AF: 0.232

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.484

Gnomad SAS AF: 0.543

Gnomad FIN AF: 0.569

Gnomad MID AF: 0.647

Gnomad NFE AF: 0.551

Gnomad OTH AF: 0.523

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

GnomAD4 genome AF: 0.467 AC: 71061 AN: 152094 Hom.: 18258 Cov.: 32 AF XY: 0.474 AC XY: 35260 AN XY: 74360

Gnomad4 AFR AF: 0.231

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.626

Gnomad4 EAS AF: 0.485

Gnomad4 SAS AF: 0.543

Gnomad4 FIN AF: 0.569

Gnomad4 NFE AF: 0.551

Gnomad4 OTH AF: 0.518

Alfa AF: 0.462 Hom.: 2531

Bravo AF: 0.458

Asia WGS AF: 0.479 AC: 1665 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	3.8
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: rs10934254; hg19: chr3-113841634;