12-41664523-A-G

Variant names:

• chr12-41664523-A-G
• rs11610493

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 0.3 in 151,996 control chromosomes in the GnomAD database, including 7,475 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 0.30 (7475 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0510
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.51 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: 0.300 AC: 45558 AN: 151878 Hom.: 7461 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.457

Gnomad ASJ AF: 0.349

Gnomad EAS AF: 0.527

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.335

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.303

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.300 AC: 45602 AN: 151996 Hom.: 7475 Cov.: 32 AF XY: 0.303 AC XY: 22488 AN XY: 74282

African (AFR) AF: 0.196 AC: 8115 AN: 41486

American (AMR) AF: 0.457 AC: 6979 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.349 AC: 1209 AN: 3468

East Asian (EAS) AF: 0.527 AC: 2716 AN: 5156

South Asian (SAS) AF: 0.291 AC: 1400 AN: 4806

European-Finnish (FIN) AF: 0.335 AC: 3540 AN: 10556

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.303 AC: 20559 AN: 67946

Other (OTH) AF: 0.332 AC: 701 AN: 2110

Alfa AF: 0.263 Hom.: 1454

Bravo AF: 0.309

Asia WGS AF: 0.427 AC: 1481 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.6
DANN	Benign	0.80
PhyloP100		-0.051

Splicing

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

Other links and lift over

dbSNP: rs11610493; hg19: chr12-42058325;