chr12-41778180-C-T

Variant names:

• chr12-41778180-C-T
• rs871392

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 0.148 in 152,144 control chromosomes in the GnomAD database, including 1,972 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 0.15 (1972 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 11 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.262 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.148 AC: 22539 AN: 152026 Hom.: 1975 Cov.: 33

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.160

Gnomad AMR AF: 0.230

Gnomad ASJ AF: 0.155

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.0861

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.158

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

GnomAD4 genome AF: 0.148 AC: 22542 AN: 152144 Hom.: 1972 Cov.: 33 AF XY: 0.153 AC XY: 11378 AN XY: 74386

African (AFR) AF: 0.172 AC: 7145 AN: 41504

American (AMR) AF: 0.230 AC: 3519 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.155 AC: 538 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1415 AN: 5160

South Asian (SAS) AF: 0.207 AC: 996 AN: 4816

European-Finnish (FIN) AF: 0.0861 AC: 913 AN: 10608

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7465 AN: 67994

Other (OTH) AF: 0.158 AC: 334 AN: 2114

Alfa AF: 0.131 Hom.: 4618

Bravo AF: 0.161

Asia WGS AF: 0.232 AC: 807 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.57
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs871392; hg19: chr12-42171982;