rs4336908

Variant names:

• chr1-202939408-G-A
• rs4336908

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 0.171 in 152,150 control chromosomes in the GnomAD database, including 2,569 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 0.17 (2569 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.162

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.317 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: 0.171 AC: 26036 AN: 152032 Hom.: 2559 Cov.: 32

Gnomad AFR AF: 0.0891

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.144

Gnomad ASJ AF: 0.182

Gnomad EAS AF: 0.289

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.187

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.205

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.171 AC: 26065 AN: 152150 Hom.: 2569 Cov.: 32 AF XY: 0.174 AC XY: 12916 AN XY: 74374

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.144

Gnomad4 ASJ AF: 0.182

Gnomad4 EAS AF: 0.290

Gnomad4 SAS AF: 0.331

Gnomad4 FIN AF: 0.187

Gnomad4 NFE AF: 0.205

Gnomad4 OTH AF: 0.160

Alfa AF: 0.185 Hom.: 1222

Bravo AF: 0.158

Asia WGS AF: 0.310 AC: 1080 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.6
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4336908; hg19: chr1-202908536;