12-60403922-A-T

Variant names:

• chr12-60403922-A-T
• rs10506410

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 0.213 in 152,090 control chromosomes in the GnomAD database, including 3,602 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 0.21 (3602 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.395
• Publications: 8 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.318 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: 0.213 AC: 32349 AN: 151968 Hom.: 3596 Cov.: 32

Gnomad AFR AF: 0.203

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.254

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.111

Gnomad SAS AF: 0.331

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.182

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.213 AC: 32363 AN: 152090 Hom.: 3602 Cov.: 32 AF XY: 0.212 AC XY: 15775 AN XY: 74340

African (AFR) AF: 0.202 AC: 8399 AN: 41508

American (AMR) AF: 0.254 AC: 3867 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 611 AN: 3470

East Asian (EAS) AF: 0.111 AC: 574 AN: 5166

South Asian (SAS) AF: 0.331 AC: 1601 AN: 4830

European-Finnish (FIN) AF: 0.172 AC: 1818 AN: 10594

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.217 AC: 14770 AN: 67964

Other (OTH) AF: 0.202 AC: 426 AN: 2112

Alfa AF: 0.200 Hom.: 400

Bravo AF: 0.219

Asia WGS AF: 0.210 AC: 732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.0
DANN	Benign	0.37
PhyloP100		-0.40

Splicing

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

Other links and lift over

dbSNP: rs10506410; hg19: chr12-60797703;