rs2345981

Variant names:

• chr6-62500036-G-A
• rs2345981

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 0.31 in 151,984 control chromosomes in the GnomAD database, including 8,128 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 (8128 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.171
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.406 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47136 AN: 151866 Hom.: 8133 Cov.: 32

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.294

Gnomad ASJ AF: 0.334

Gnomad EAS AF: 0.421

Gnomad SAS AF: 0.317

Gnomad FIN AF: 0.399

Gnomad MID AF: 0.290

Gnomad NFE AF: 0.383

Gnomad OTH AF: 0.329

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

GnomAD4 genome AF: 0.310 AC: 47130 AN: 151984 Hom.: 8128 Cov.: 32 AF XY: 0.311 AC XY: 23139 AN XY: 74308

African (AFR) AF: 0.156 AC: 6485 AN: 41466

American (AMR) AF: 0.294 AC: 4481 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.334 AC: 1159 AN: 3470

East Asian (EAS) AF: 0.420 AC: 2169 AN: 5160

South Asian (SAS) AF: 0.318 AC: 1533 AN: 4824

European-Finnish (FIN) AF: 0.399 AC: 4203 AN: 10546

Middle Eastern (MID) AF: 0.295 AC: 86 AN: 292

European-Non Finnish (NFE) AF: 0.383 AC: 26000 AN: 67944

Other (OTH) AF: 0.326 AC: 689 AN: 2112

Alfa AF: 0.368 Hom.: 13770

Bravo AF: 0.295

Asia WGS AF: 0.303 AC: 1053 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.91
DANN	Benign	0.74
PhyloP100		-0.17

Splicing

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

Other links and lift over

dbSNP: rs2345981; hg19: chr6-63209941;