rs4659720

Positions:

• chr1-236786561-T-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 0.0689 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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;