chr2-212545341-G-A

Variant names:

• chr2-212545341-G-A
• rs6435711

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 0.499 in 152,080 control chromosomes in the GnomAD database, including 21,615 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 0.50 (21615 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.867
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.769 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: 0.499 AC: 75767 AN: 151962 Hom.: 21548 Cov.: 32

Gnomad AFR AF: 0.775

Gnomad AMI AF: 0.464

Gnomad AMR AF: 0.325

Gnomad ASJ AF: 0.406

Gnomad EAS AF: 0.0744

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.436

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.432

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.499 AC: 75888 AN: 152080 Hom.: 21615 Cov.: 32 AF XY: 0.490 AC XY: 36441 AN XY: 74340

African (AFR) AF: 0.776 AC: 32207 AN: 41504

American (AMR) AF: 0.325 AC: 4959 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.406 AC: 1409 AN: 3472

East Asian (EAS) AF: 0.0748 AC: 388 AN: 5188

South Asian (SAS) AF: 0.317 AC: 1527 AN: 4820

European-Finnish (FIN) AF: 0.436 AC: 4611 AN: 10568

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.432 AC: 29370 AN: 67950

Other (OTH) AF: 0.429 AC: 903 AN: 2104

Alfa AF: 0.450 Hom.: 8479

Bravo AF: 0.502

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.35
DANN	Benign	0.30
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs6435711; hg19: chr2-213410065;