rs457414

chr3-10161200-C-Achr3-10161200-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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;