3-114122787-G-A

Variant names:

• chr3-114122787-G-A
• rs10934254

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.231 AC: 9604 AN: 41504

American (AMR) AF: 0.585 AC: 8945 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2170 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2503 AN: 5164

South Asian (SAS) AF: 0.543 AC: 2614 AN: 4812

European-Finnish (FIN) AF: 0.569 AC: 6013 AN: 10572

Middle Eastern (MID) AF: 0.634 AC: 184 AN: 290

European-Non Finnish (NFE) AF: 0.551 AC: 37460 AN: 67970

Other (OTH) AF: 0.518 AC: 1094 AN: 2110

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
PhyloP100		0.060

Splicing

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

Other links and lift over

dbSNP: rs10934254; hg19: chr3-113841634;