rs4660687

Positions:

• chr1-42911868-A-C

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 0.37 in 152,082 control chromosomes in the GnomAD database, including 10,692 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 0.37 (10692 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.301

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.54).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.429 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: 0.370 AC: 56221 AN: 151964 Hom.: 10689 Cov.: 31

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.437

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.306

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.378

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

GnomAD4 genome AF: 0.370 AC: 56239 AN: 152082 Hom.: 10692 Cov.: 31 AF XY: 0.372 AC XY: 27668 AN XY: 74346

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.437

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.306

Gnomad4 SAS AF: 0.424

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.374

Alfa AF: 0.400 Hom.: 5773

Bravo AF: 0.369

Asia WGS AF: 0.358 AC: 1249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.54
CADD	Benign	9.1
DANN	Benign	0.95

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4660687; hg19: chr1-43377539; COSMIC: COSV59941485;