rs6435203

Positions:

• chr2-203746472-G-A

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 0.689 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.658

Gnomad4 AMR AF: 0.661

Gnomad4 ASJ AF: 0.662

Gnomad4 EAS AF: 0.409

Gnomad4 SAS AF: 0.836

Gnomad4 FIN AF: 0.758

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.678

Alfa AF: 0.721 Hom.: 18048

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6435203; hg19: chr2-204611195;