rs2209067

Variant names:

• chr10-44221021-G-A
• rs2209067

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 0.18 in 152,086 control chromosomes in the GnomAD database, including 2,550 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 0.18 (2550 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.208
• Publications: 4 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 (AFR) allele frequency at 95% confidence interval = 0.182 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: 0.180 AC: 27353 AN: 151968 Hom.: 2544 Cov.: 32

Gnomad AFR AF: 0.186

Gnomad AMI AF: 0.0768

Gnomad AMR AF: 0.181

Gnomad ASJ AF: 0.148

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.120

Gnomad FIN AF: 0.200

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.184

Gnomad OTH AF: 0.194

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

GnomAD4 genome AF: 0.180 AC: 27378 AN: 152086 Hom.: 2550 Cov.: 32 AF XY: 0.181 AC XY: 13463 AN XY: 74338

African (AFR) AF: 0.186 AC: 7716 AN: 41496

American (AMR) AF: 0.181 AC: 2758 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.148 AC: 515 AN: 3472

East Asian (EAS) AF: 0.132 AC: 684 AN: 5180

South Asian (SAS) AF: 0.121 AC: 583 AN: 4812

European-Finnish (FIN) AF: 0.200 AC: 2113 AN: 10576

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.184 AC: 12484 AN: 67974

Other (OTH) AF: 0.192 AC: 404 AN: 2108

Alfa AF: 0.174 Hom.: 306

Bravo AF: 0.181

Asia WGS AF: 0.139 AC: 483 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.3
DANN	Benign	0.61
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs2209067; hg19: chr10-44716469;