rs6726821

Variant names:

• chr2-165721604-T-G
• rs6726821

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 0.396 in 151,936 control chromosomes in the GnomAD database, including 12,983 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 0.40 (12983 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• 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: 0.396 AC: 60152 AN: 151818 Hom.: 12972 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.458

Gnomad EAS AF: 0.356

Gnomad SAS AF: 0.326

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.489

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.396 AC: 60185 AN: 151936 Hom.: 12983 Cov.: 32 AF XY: 0.399 AC XY: 29597 AN XY: 74244

African (AFR) AF: 0.231 AC: 9567 AN: 41464

American (AMR) AF: 0.356 AC: 5431 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.458 AC: 1587 AN: 3466

East Asian (EAS) AF: 0.357 AC: 1842 AN: 5164

South Asian (SAS) AF: 0.326 AC: 1568 AN: 4806

European-Finnish (FIN) AF: 0.519 AC: 5473 AN: 10540

Middle Eastern (MID) AF: 0.327 AC: 96 AN: 294

European-Non Finnish (NFE) AF: 0.489 AC: 33218 AN: 67930

Other (OTH) AF: 0.401 AC: 847 AN: 2112

Alfa AF: 0.451 Hom.: 24996

Bravo AF: 0.374

Asia WGS AF: 0.337 AC: 1169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	5.0
DANN	Benign	0.44
PhyloP100		1.7

Splicing

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

Other links and lift over

dbSNP: rs6726821; hg19: chr2-166578114;