rs4839335

Variant names:

• chr1-113691249-G-A
• rs4839335

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 0.732 in 152,034 control chromosomes in the GnomAD database, including 41,216 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 0.73 (41216 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.776 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: 0.731 AC: 111117 AN: 151916 Hom.: 41177 Cov.: 31

Gnomad AFR AF: 0.783

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.623

Gnomad ASJ AF: 0.763

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.763

Gnomad FIN AF: 0.687

Gnomad MID AF: 0.720

Gnomad NFE AF: 0.756

Gnomad OTH AF: 0.721

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

GnomAD4 genome AF: 0.732 AC: 111218 AN: 152034 Hom.: 41216 Cov.: 31 AF XY: 0.726 AC XY: 53973 AN XY: 74314

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.623

Gnomad4 ASJ AF: 0.763

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.763

Gnomad4 FIN AF: 0.687

Gnomad4 NFE AF: 0.756

Gnomad4 OTH AF: 0.722

Alfa AF: 0.754 Hom.: 25174

Bravo AF: 0.722

Asia WGS AF: 0.611 AC: 2125 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.70
DANN	Benign	0.23

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4839335; hg19: chr1-114233871;