rs2734871

chr2-136112303-G-Achr2-136112303-G-T

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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

Gnomad4 AFR AF: 0.486

Gnomad4 AMR AF: 0.279

Gnomad4 ASJ AF: 0.150

Gnomad4 EAS AF: 0.0375

Gnomad4 SAS AF: 0.268

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.225

Gnomad4 OTH AF: 0.253

Alfa AF: 0.195 Hom.: 770

Bravo AF: 0.308

Asia WGS AF: 0.167 AC: 578 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	2.1
Dann	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2734871; hg19: chr2-136869873;