rs2844731

Variant names:

• chr6-30449208-G-A
• rs2844731

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 0.114 in 152,194 control chromosomes in the GnomAD database, including 1,318 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 0.11 (1318 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.371
• Publications: 10 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 (AMR) allele frequency at 95% confidence interval = 0.149 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: 0.114 AC: 17408 AN: 152076 Hom.: 1316 Cov.: 32

Gnomad AFR AF: 0.0294

Gnomad AMI AF: 0.217

Gnomad AMR AF: 0.154

Gnomad ASJ AF: 0.110

Gnomad EAS AF: 0.0812

Gnomad SAS AF: 0.136

Gnomad FIN AF: 0.164

Gnomad MID AF: 0.162

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.114 AC: 17412 AN: 152194 Hom.: 1318 Cov.: 32 AF XY: 0.116 AC XY: 8600 AN XY: 74406

African (AFR) AF: 0.0293 AC: 1218 AN: 41524

American (AMR) AF: 0.154 AC: 2357 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.110 AC: 381 AN: 3470

East Asian (EAS) AF: 0.0809 AC: 419 AN: 5182

South Asian (SAS) AF: 0.137 AC: 658 AN: 4814

European-Finnish (FIN) AF: 0.164 AC: 1732 AN: 10580

Middle Eastern (MID) AF: 0.161 AC: 47 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10148 AN: 68004

Other (OTH) AF: 0.120 AC: 254 AN: 2110

Alfa AF: 0.134 Hom.: 387

Bravo AF: 0.112

Asia WGS AF: 0.100 AC: 349 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	1.3
DANN	Benign	0.52
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs2844731; hg19: chr6-30416985;