rs4654712

Variant names:

• chr1-229059346-T-A
• rs4654712

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 0.579 in 152,110 control chromosomes in the GnomAD database, including 25,603 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 (25603 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.183

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.588 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: 0.579 AC: 88001 AN: 151992 Hom.: 25574 Cov.: 34

Gnomad AFR AF: 0.564

Gnomad AMI AF: 0.591

Gnomad AMR AF: 0.565

Gnomad ASJ AF: 0.540

Gnomad EAS AF: 0.576

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.593

Gnomad OTH AF: 0.545

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

GnomAD4 genome AF: 0.579 AC: 88079 AN: 152110 Hom.: 25603 Cov.: 34 AF XY: 0.580 AC XY: 43165 AN XY: 74370

Gnomad4 AFR AF: 0.564

Gnomad4 AMR AF: 0.566

Gnomad4 ASJ AF: 0.540

Gnomad4 EAS AF: 0.575

Gnomad4 SAS AF: 0.578

Gnomad4 FIN AF: 0.588

Gnomad4 NFE AF: 0.593

Gnomad4 OTH AF: 0.549

Alfa AF: 0.591 Hom.: 3342

Bravo AF: 0.574

Asia WGS AF: 0.569 AC: 1982 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.74
DANN	Benign	0.66

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4654712; hg19: chr1-229195093; COSMIC: COSV69481192;