2-165726734-C-T

Variant names:

• chr2-165726734-C-T
• rs6710518

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 0.389 in 151,160 control chromosomes in the GnomAD database, including 12,689 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 0.39 (12689 hom., cov: 28)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0290

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.485 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: 0.390 AC: 58846 AN: 151044 Hom.: 12680 Cov.: 28

Gnomad AFR AF: 0.205

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.355

Gnomad SAS AF: 0.328

Gnomad FIN AF: 0.522

Gnomad MID AF: 0.318

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.390

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

GnomAD4 genome AF: 0.389 AC: 58873 AN: 151160 Hom.: 12689 Cov.: 28 AF XY: 0.393 AC XY: 29006 AN XY: 73876

Gnomad4 AFR AF: 0.205

Gnomad4 AMR AF: 0.355

Gnomad4 ASJ AF: 0.458

Gnomad4 EAS AF: 0.356

Gnomad4 SAS AF: 0.328

Gnomad4 FIN AF: 0.522

Gnomad4 NFE AF: 0.489

Gnomad4 OTH AF: 0.394

Alfa AF: 0.460 Hom.: 36208

Bravo AF: 0.366

Asia WGS AF: 0.334 AC: 1161 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6710518; hg19: chr2-166583244;