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. Variant got -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

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 (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

Gnomad4 AFR AF: 0.299

Gnomad4 AMR AF: 0.655

Gnomad4 ASJ AF: 0.738

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.558

Gnomad4 FIN AF: 0.748

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.599

Alfa AF: 0.645 Hom.: 31752

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs457414; hg19: chr3-10202884;