chr2-238212011-T-C

Variant names:

• chr2-238212011-T-C
• rs2341697

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 0.4 in 151,698 control chromosomes in the GnomAD database, including 13,808 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 0.40 (13808 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0970
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.629 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: 0.399 AC: 60527 AN: 151580 Hom.: 13773 Cov.: 30

Gnomad AFR AF: 0.605

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.430

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.647

Gnomad SAS AF: 0.310

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.404

Gnomad NFE AF: 0.271

Gnomad OTH AF: 0.389

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

GnomAD4 genome AF: 0.400 AC: 60619 AN: 151698 Hom.: 13808 Cov.: 30 AF XY: 0.403 AC XY: 29887 AN XY: 74134

African (AFR) AF: 0.605 AC: 25030 AN: 41368

American (AMR) AF: 0.431 AC: 6562 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1385 AN: 3468

East Asian (EAS) AF: 0.647 AC: 3341 AN: 5164

South Asian (SAS) AF: 0.311 AC: 1496 AN: 4818

European-Finnish (FIN) AF: 0.317 AC: 3327 AN: 10484

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.271 AC: 18372 AN: 67862

Other (OTH) AF: 0.393 AC: 826 AN: 2104

Alfa AF: 0.317 Hom.: 20444

Bravo AF: 0.418

Asia WGS AF: 0.464 AC: 1610 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	2.2
DANN	Benign	0.38
PhyloP100		0.097

Splicing

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

Other links and lift over

dbSNP: rs2341697; hg19: chr2-239120652;