rs2734990

Variant names:

• chr6-29844728-A-T
• rs2734990

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 0.306 in 152,134 control chromosomes in the GnomAD database, including 7,465 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 0.31 (7465 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.995
• Publications: 21 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.407 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: 0.306 AC: 46520 AN: 152016 Hom.: 7453 Cov.: 31

Gnomad AFR AF: 0.376

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.423

Gnomad SAS AF: 0.418

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.315

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

GnomAD4 genome AF: 0.306 AC: 46571 AN: 152134 Hom.: 7465 Cov.: 31 AF XY: 0.310 AC XY: 23046 AN XY: 74378

African (AFR) AF: 0.376 AC: 15600 AN: 41492

American (AMR) AF: 0.366 AC: 5592 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3466

East Asian (EAS) AF: 0.422 AC: 2186 AN: 5180

South Asian (SAS) AF: 0.418 AC: 2012 AN: 4818

European-Finnish (FIN) AF: 0.226 AC: 2393 AN: 10582

Middle Eastern (MID) AF: 0.333 AC: 98 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16813 AN: 67990

Other (OTH) AF: 0.323 AC: 684 AN: 2116

Alfa AF: 0.266 Hom.: 848

Bravo AF: 0.317

Asia WGS AF: 0.495 AC: 1719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.2
DANN	Benign	0.24
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs2734990; hg19: chr6-29812505;