chr2-31415003-C-T

Variant names:

• chr2-31415003-C-T
• rs206812

Variant summary

Our verdict is Benign. The variant received -14 ACMG points: 0P and 14B. BP4_Strong BP6_Moderate 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. Variant has been reported in ClinVar as Benign (★).

• 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 -14 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BP6: Variant 2-31415003-C-T is Benign according to our data. Variant chr2-31415003-C-T is described in ClinVar as Benign. ClinVar VariationId is 1260445.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.497 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

ClinVar submissions

Significance: Benign

Revision: criteria provided, single submitter

Pathogenic	VUS	Benign	Condition
-	-	1	not provided (1)

Computational scores

Source: dbNSFP v4.9

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;