rs6436346

Variant names:

• chr2-222809603-G-A
• rs6436346

Your query was ambiguous. Multiple possible variants found:

• chr2-222809603-G-A
• chr2-222809603-G-C
• chr2-222809603-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 0.707 in 152,034 control chromosomes in the GnomAD database, including 38,493 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 0.71 (38493 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.140

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.812 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: 0.707 AC: 107359 AN: 151916 Hom.: 38442 Cov.: 31

Gnomad AFR AF: 0.819

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.621

Gnomad ASJ AF: 0.680

Gnomad EAS AF: 0.600

Gnomad SAS AF: 0.677

Gnomad FIN AF: 0.629

Gnomad MID AF: 0.764

Gnomad NFE AF: 0.681

Gnomad OTH AF: 0.694

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

GnomAD4 genome AF: 0.707 AC: 107461 AN: 152034 Hom.: 38493 Cov.: 31 AF XY: 0.702 AC XY: 52151 AN XY: 74310

Gnomad4 AFR AF: 0.820

Gnomad4 AMR AF: 0.620

Gnomad4 ASJ AF: 0.680

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.677

Gnomad4 FIN AF: 0.629

Gnomad4 NFE AF: 0.681

Gnomad4 OTH AF: 0.693

Alfa AF: 0.685 Hom.: 72405

Bravo AF: 0.710

Asia WGS AF: 0.609 AC: 2120 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.6
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6436346; hg19: chr2-223674322;