rs12219216

Variant names:

• chr10-107318735-A-G
• rs12219216

Your query was ambiguous. Multiple possible variants found:

• chr10-107318735-A-G
• chr10-107318735-A-T

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 0.439 in 151,950 control chromosomes in the GnomAD database, including 17,173 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 0.44 (17173 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.392
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.440 AC: 66752 AN: 151832 Hom.: 17173 Cov.: 31

Gnomad AFR AF: 0.157

Gnomad AMI AF: 0.606

Gnomad AMR AF: 0.468

Gnomad ASJ AF: 0.559

Gnomad EAS AF: 0.398

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.509

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.439 AC: 66761 AN: 151950 Hom.: 17173 Cov.: 31 AF XY: 0.437 AC XY: 32462 AN XY: 74248

African (AFR) AF: 0.157 AC: 6500 AN: 41474

American (AMR) AF: 0.468 AC: 7135 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 1940 AN: 3470

East Asian (EAS) AF: 0.399 AC: 2062 AN: 5162

South Asian (SAS) AF: 0.452 AC: 2177 AN: 4818

European-Finnish (FIN) AF: 0.509 AC: 5352 AN: 10522

Middle Eastern (MID) AF: 0.605 AC: 178 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39887 AN: 67932

Other (OTH) AF: 0.464 AC: 980 AN: 2112

Alfa AF: 0.478 Hom.: 3131

Bravo AF: 0.422

Asia WGS AF: 0.364 AC: 1261 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.4
DANN	Benign	0.77
PhyloP100		-0.39

Splicing

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

Other links and lift over

dbSNP: rs12219216; hg19: chr10-109078493;