rs457414

Variant names:

• chr3-10161200-C-A
• rs457414

Your query was ambiguous. Multiple possible variants found:

• chr3-10161200-C-A
• chr3-10161200-C-T

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 0.577 in 152,046 control chromosomes in the GnomAD database, including 27,638 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 0.58 (27638 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0200
• Publications: 22 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 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: 0.577 AC: 87653 AN: 151928 Hom.: 27623 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.655

Gnomad ASJ AF: 0.738

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.748

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.606

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

GnomAD4 genome AF: 0.577 AC: 87697 AN: 152046 Hom.: 27638 Cov.: 32 AF XY: 0.584 AC XY: 43378 AN XY: 74318

African (AFR) AF: 0.299 AC: 12381 AN: 41450

American (AMR) AF: 0.655 AC: 9994 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.738 AC: 2561 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4065 AN: 5174

South Asian (SAS) AF: 0.558 AC: 2688 AN: 4814

European-Finnish (FIN) AF: 0.748 AC: 7922 AN: 10588

Middle Eastern (MID) AF: 0.677 AC: 199 AN: 294

European-Non Finnish (NFE) AF: 0.678 AC: 46079 AN: 67982

Other (OTH) AF: 0.599 AC: 1264 AN: 2110

Alfa AF: 0.634 Hom.: 45781

Bravo AF: 0.558

Asia WGS AF: 0.658 AC: 2290 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	0.91
DANN	Benign	0.68
PhyloP100		0.020

Splicing

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

Other links and lift over

dbSNP: rs457414; hg19: chr3-10202884;