2-31415003-C-T

Variant names:

• chr2-31415003-C-T
• rs206812

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 0.489 in 152,112 control chromosomes in the GnomAD database, including 18,321 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 0.49 (18321 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.17
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 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: 0.489 AC: 74313 AN: 151994 Hom.: 18306 Cov.: 32

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.525

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.502

Gnomad OTH AF: 0.492

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

GnomAD4 genome AF: 0.489 AC: 74372 AN: 152112 Hom.: 18321 Cov.: 32 AF XY: 0.488 AC XY: 36283 AN XY: 74342

African (AFR) AF: 0.483 AC: 20051 AN: 41474

American (AMR) AF: 0.493 AC: 7536 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.552 AC: 1915 AN: 3472

East Asian (EAS) AF: 0.352 AC: 1819 AN: 5166

South Asian (SAS) AF: 0.361 AC: 1742 AN: 4830

European-Finnish (FIN) AF: 0.525 AC: 5547 AN: 10574

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.502 AC: 34099 AN: 67988

Other (OTH) AF: 0.488 AC: 1029 AN: 2108

Alfa AF: 0.499 Hom.: 2755

Bravo AF: 0.490

Asia WGS AF: 0.336 AC: 1171 AN: 3478

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Dec 08, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	10
DANN	Benign	0.67
PhyloP100		1.2
PromoterAI		0.091	Neutral

Splicing

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

Other links and lift over

dbSNP: rs206812; hg19: chr2-31637869;