rs231729

Variant names:

• chr2-203879078-T-A
• rs231729

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 0.38 in 152,066 control chromosomes in the GnomAD database, including 11,470 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 0.38 (11470 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.05
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.573 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: 0.380 AC: 57735 AN: 151948 Hom.: 11450 Cov.: 32

Gnomad AFR AF: 0.415

Gnomad AMI AF: 0.378

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.257

Gnomad EAS AF: 0.591

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.503

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.336

Gnomad OTH AF: 0.330

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

GnomAD4 genome AF: 0.380 AC: 57805 AN: 152066 Hom.: 11470 Cov.: 32 AF XY: 0.387 AC XY: 28785 AN XY: 74332

African (AFR) AF: 0.415 AC: 17199 AN: 41464

American (AMR) AF: 0.393 AC: 6002 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.257 AC: 890 AN: 3468

East Asian (EAS) AF: 0.590 AC: 3057 AN: 5180

South Asian (SAS) AF: 0.285 AC: 1377 AN: 4824

European-Finnish (FIN) AF: 0.503 AC: 5311 AN: 10552

Middle Eastern (MID) AF: 0.223 AC: 65 AN: 292

European-Non Finnish (NFE) AF: 0.336 AC: 22866 AN: 67980

Other (OTH) AF: 0.329 AC: 693 AN: 2104

Alfa AF: 0.367 Hom.: 1271

Bravo AF: 0.377

Asia WGS AF: 0.403 AC: 1397 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.027
DANN	Benign	0.36
PhyloP100		-4.0

Splicing

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

Other links and lift over

dbSNP: rs231729; hg19: chr2-204743801;