rs4661281

Variant names:

• chr1-223108368-C-T
• rs4661281

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 0.337 in 151,906 control chromosomes in the GnomAD database, including 9,941 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 0.34 (9941 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

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 = 0.427 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: 0.337 AC: 51211 AN: 151788 Hom.: 9940 Cov.: 32

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.499

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.402

Gnomad EAS AF: 0.208

Gnomad SAS AF: 0.422

Gnomad FIN AF: 0.497

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.431

Gnomad OTH AF: 0.338

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

GnomAD4 genome AF: 0.337 AC: 51239 AN: 151906 Hom.: 9941 Cov.: 32 AF XY: 0.340 AC XY: 25244 AN XY: 74252

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.324

Gnomad4 ASJ AF: 0.402

Gnomad4 EAS AF: 0.208

Gnomad4 SAS AF: 0.423

Gnomad4 FIN AF: 0.497

Gnomad4 NFE AF: 0.431

Gnomad4 OTH AF: 0.338

Alfa AF: 0.391 Hom.: 1562

Bravo AF: 0.313

Asia WGS AF: 0.301 AC: 1046 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	1.2
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4661281; hg19: chr1-223281710;