12-100472862-G-A

Variant names:

• chr12-100472862-G-A
• rs3863377

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0161 in 152,174 control chromosomes in the GnomAD database, including 25 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 0.016 (25 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.651
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0161 (2444/152174) while in subpopulation NFE AF = 0.0248 (1687/68004). AF 95% confidence interval is 0.0238. There are 25 homozygotes in GnomAd4. There are 1146 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 25 gene

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: 0.0161 AC: 2443 AN: 152056 Hom.: 25 Cov.: 32

Gnomad AFR AF: 0.00928

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.00808

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.00497

Gnomad FIN AF: 0.00490

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0105

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

GnomAD4 genome AF: 0.0161 AC: 2444 AN: 152174 Hom.: 25 Cov.: 32 AF XY: 0.0154 AC XY: 1146 AN XY: 74386

African (AFR) AF: 0.00928 AC: 385 AN: 41508

American (AMR) AF: 0.0151 AC: 231 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.00808 AC: 28 AN: 3466

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5168

South Asian (SAS) AF: 0.00498 AC: 24 AN: 4822

European-Finnish (FIN) AF: 0.00490 AC: 52 AN: 10602

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 294

European-Non Finnish (NFE) AF: 0.0248 AC: 1687 AN: 68004

Other (OTH) AF: 0.0104 AC: 22 AN: 2110

Alfa AF: 0.0216 Hom.: 8

Bravo AF: 0.0157

Asia WGS AF: 0.00289 AC: 10 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.28
DANN	Benign	0.57
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs3863377; hg19: chr12-100866640;