rs6729914

Variant names:

• chr2-219578794-T-C
• rs6729914

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 0.494 in 152,016 control chromosomes in the GnomAD database, including 18,817 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 0.49 (18817 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.715
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.561 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: 0.494 AC: 75026 AN: 151898 Hom.: 18812 Cov.: 32

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.507

Gnomad ASJ AF: 0.506

Gnomad EAS AF: 0.316

Gnomad SAS AF: 0.581

Gnomad FIN AF: 0.470

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.497

Gnomad OTH AF: 0.507

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

GnomAD4 genome AF: 0.494 AC: 75070 AN: 152016 Hom.: 18817 Cov.: 32 AF XY: 0.494 AC XY: 36718 AN XY: 74284

African (AFR) AF: 0.502 AC: 20799 AN: 41442

American (AMR) AF: 0.507 AC: 7747 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.506 AC: 1756 AN: 3470

East Asian (EAS) AF: 0.317 AC: 1640 AN: 5180

South Asian (SAS) AF: 0.579 AC: 2782 AN: 4808

European-Finnish (FIN) AF: 0.470 AC: 4967 AN: 10562

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.497 AC: 33793 AN: 67966

Other (OTH) AF: 0.503 AC: 1063 AN: 2114

Alfa AF: 0.499 Hom.: 59449

Bravo AF: 0.492

Asia WGS AF: 0.427 AC: 1489 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	2.2
DANN	Benign	0.71
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs6729914; hg19: chr2-220443516;