rs2734871

Variant names:

• chr2-136112303-G-A
• rs2734871

Your query was ambiguous. Multiple possible variants found:

• chr2-136112303-G-A
• chr2-136112303-G-T

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 0.289 in 152,098 control chromosomes in the GnomAD database, including 7,780 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 0.29 (7780 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.303
• Publications: 7 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.288 AC: 43837 AN: 151980 Hom.: 7759 Cov.: 32

Gnomad AFR AF: 0.486

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.0374

Gnomad SAS AF: 0.267

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.225

Gnomad OTH AF: 0.255

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

GnomAD4 genome AF: 0.289 AC: 43913 AN: 152098 Hom.: 7780 Cov.: 32 AF XY: 0.282 AC XY: 20955 AN XY: 74362

African (AFR) AF: 0.486 AC: 20162 AN: 41460

American (AMR) AF: 0.279 AC: 4272 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 520 AN: 3472

East Asian (EAS) AF: 0.0375 AC: 194 AN: 5180

South Asian (SAS) AF: 0.268 AC: 1292 AN: 4824

European-Finnish (FIN) AF: 0.127 AC: 1341 AN: 10582

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.225 AC: 15312 AN: 67982

Other (OTH) AF: 0.253 AC: 533 AN: 2110

Alfa AF: 0.204 Hom.: 864

Bravo AF: 0.308

Asia WGS AF: 0.167 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.18
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2734871; hg19: chr2-136869873;