rs4659720

Variant names:

• chr1-236786561-T-C
• rs4659720

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 0.0689 in 152,300 control chromosomes in the GnomAD database, including 756 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 0.069 (756 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.195

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 (AFR) allele frequency at 95% confidence interval = 0.174 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: 0.0687 AC: 10455 AN: 152182 Hom.: 753 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0132

Gnomad EAS AF: 0.0312

Gnomad SAS AF: 0.127

Gnomad FIN AF: 0.0222

Gnomad MID AF: 0.0665

Gnomad NFE AF: 0.0192

Gnomad OTH AF: 0.0554

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

GnomAD4 genome AF: 0.0689 AC: 10493 AN: 152300 Hom.: 756 Cov.: 33 AF XY: 0.0686 AC XY: 5108 AN XY: 74482

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.0376

Gnomad4 ASJ AF: 0.0132

Gnomad4 EAS AF: 0.0309

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.0222

Gnomad4 NFE AF: 0.0192

Gnomad4 OTH AF: 0.0605

Alfa AF: 0.0650 Hom.: 100

Bravo AF: 0.0734

Asia WGS AF: 0.0980 AC: 341 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	5.4
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4659720; hg19: chr1-236949861;