rs4660456

chr1-40773839-A-G

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.218 in 152,214 control chromosomes in the GnomAD database, including 4,278 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 0.22 (4278 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0240

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.4).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.403 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: 0.218 AC: 33130 AN: 152096 Hom.: 4269 Cov.: 32

Gnomad AFR AF: 0.101

Gnomad AMI AF: 0.418

Gnomad AMR AF: 0.338

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.418

Gnomad SAS AF: 0.420

Gnomad FIN AF: 0.225

Gnomad MID AF: 0.218

Gnomad NFE AF: 0.227

Gnomad OTH AF: 0.239

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

GnomAD4 genome AF: 0.218 AC: 33151 AN: 152214 Hom.: 4278 Cov.: 32 AF XY: 0.224 AC XY: 16651 AN XY: 74428

Gnomad4 AFR AF: 0.100

Gnomad4 AMR AF: 0.338

Gnomad4 ASJ AF: 0.243

Gnomad4 EAS AF: 0.417

Gnomad4 SAS AF: 0.418

Gnomad4 FIN AF: 0.225

Gnomad4 NFE AF: 0.227

Gnomad4 OTH AF: 0.246

Alfa AF: 0.232 Hom.: 5150

Bravo AF: 0.216

Asia WGS AF: 0.425 AC: 1477 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.40
Cadd	Benign	13
Dann	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4660456; hg19: chr1-41239511; COSMIC: COSV58129718;