2-165726734-C-T

Variant names:

• chr2-165726734-C-T
• rs6710518

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 0.389 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
• Publications: 40 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.205 AC: 8460 AN: 41204

American (AMR) AF: 0.355 AC: 5400 AN: 15190

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1588 AN: 3470

East Asian (EAS) AF: 0.356 AC: 1821 AN: 5114

South Asian (SAS) AF: 0.328 AC: 1568 AN: 4774

European-Finnish (FIN) AF: 0.522 AC: 5418 AN: 10372

Middle Eastern (MID) AF: 0.324 AC: 94 AN: 290

European-Non Finnish (NFE) AF: 0.489 AC: 33139 AN: 67734

Other (OTH) AF: 0.394 AC: 827 AN: 2100

Alfa AF: 0.449 Hom.: 66393

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
PhyloP100		0.029

Splicing

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

Other links and lift over

dbSNP: rs6710518; hg19: chr2-166583244;