rs4659720

Variant names:

• chr1-236786561-T-C
• rs4659720

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.178 AC: 7390 AN: 41550

American (AMR) AF: 0.0376 AC: 575 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0132 AC: 46 AN: 3472

East Asian (EAS) AF: 0.0309 AC: 160 AN: 5180

South Asian (SAS) AF: 0.127 AC: 614 AN: 4830

European-Finnish (FIN) AF: 0.0222 AC: 236 AN: 10628

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0192 AC: 1308 AN: 68016

Other (OTH) AF: 0.0605 AC: 128 AN: 2114

Alfa AF: 0.0375 Hom.: 155

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
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs4659720; hg19: chr1-236949861;