rs6435203

Variant names:

• chr2-203746472-G-A
• rs6435203

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 0.689 in 152,060 control chromosomes in the GnomAD database, including 36,491 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 0.69 (36491 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.685
• Publications: 24 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.815 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: 0.689 AC: 104715 AN: 151942 Hom.: 36482 Cov.: 31

Gnomad AFR AF: 0.658

Gnomad AMI AF: 0.679

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.409

Gnomad SAS AF: 0.837

Gnomad FIN AF: 0.758

Gnomad MID AF: 0.696

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.678

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

GnomAD4 genome AF: 0.689 AC: 104769 AN: 152060 Hom.: 36491 Cov.: 31 AF XY: 0.690 AC XY: 51278 AN XY: 74324

African (AFR) AF: 0.658 AC: 27268 AN: 41458

American (AMR) AF: 0.661 AC: 10107 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2298 AN: 3472

East Asian (EAS) AF: 0.409 AC: 2110 AN: 5154

South Asian (SAS) AF: 0.836 AC: 4028 AN: 4816

European-Finnish (FIN) AF: 0.758 AC: 8010 AN: 10568

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48698 AN: 67976

Other (OTH) AF: 0.678 AC: 1431 AN: 2112

Alfa AF: 0.719 Hom.: 20009

Bravo AF: 0.675

Asia WGS AF: 0.663 AC: 2305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	8.6
DANN	Benign	0.83
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs6435203; hg19: chr2-204611195;