rs436346

Variant names:

• chr1-101500389-G-A
• rs436346

Your query was ambiguous. Multiple possible variants found:

• chr1-101500389-G-A
• chr1-101500389-G-C
• chr1-101500389-G-T

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 0.795 in 151,868 control chromosomes in the GnomAD database, including 48,403 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 0.79 (48403 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.218

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.795 AC: 120619 AN: 151750 Hom.: 48399 Cov.: 29

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.877

Gnomad AMR AF: 0.660

Gnomad ASJ AF: 0.875

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.732

Gnomad FIN AF: 0.835

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.845

Gnomad OTH AF: 0.826

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

GnomAD4 genome AF: 0.795 AC: 120661 AN: 151868 Hom.: 48403 Cov.: 29 AF XY: 0.793 AC XY: 58841 AN XY: 74208

Gnomad4 AFR AF: 0.738

Gnomad4 AMR AF: 0.659

Gnomad4 ASJ AF: 0.875

Gnomad4 EAS AF: 0.870

Gnomad4 SAS AF: 0.731

Gnomad4 FIN AF: 0.835

Gnomad4 NFE AF: 0.845

Gnomad4 OTH AF: 0.827

Alfa AF: 0.815 Hom.: 13424

Bravo AF: 0.776

Asia WGS AF: 0.779 AC: 2712 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	3.3
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs436346; hg19: chr1-101965945;