2-15753767-G-T

Variant names:

• chr2-15753767-G-T
• rs6705499

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 0.364 in 151,976 control chromosomes in the GnomAD database, including 10,780 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 0.36 (10780 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.449 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: 0.364 AC: 55247 AN: 151858 Hom.: 10773 Cov.: 31

Gnomad AFR AF: 0.215

Gnomad AMI AF: 0.395

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.466

Gnomad EAS AF: 0.330

Gnomad SAS AF: 0.296

Gnomad FIN AF: 0.409

Gnomad MID AF: 0.456

Gnomad NFE AF: 0.426

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.364 AC: 55299 AN: 151976 Hom.: 10780 Cov.: 31 AF XY: 0.364 AC XY: 27020 AN XY: 74244

Gnomad4 AFR AF: 0.215

Gnomad4 AMR AF: 0.458

Gnomad4 ASJ AF: 0.466

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.298

Gnomad4 FIN AF: 0.409

Gnomad4 NFE AF: 0.426

Gnomad4 OTH AF: 0.404

Alfa AF: 0.415 Hom.: 27297

Bravo AF: 0.363

Asia WGS AF: 0.297 AC: 1034 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.082
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6705499; hg19: chr2-15893891;