chr12-121105208-C-T

Variant names:

• chr12-121105208-C-T
• rs1796415
• ENST00000837362.1:n.128-4479G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000837362.1(ENSG00000308932):​n.128-4479G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.843 in 152,154 control chromosomes in the GnomAD database, including 54,836 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 0.84 (54836 hom., cov: 32)
• Consequence: ENSG00000308932 ENST00000837362.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22
• Publications: 5 publications found

Genes affected

ENSG00000308932 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.972 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000837362.1. You can select a different transcript below to see updated ACMG assignments.

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
	ENSG00000308932	ENST00000837362.1		n.128-4479G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.843 AC: 128135 AN: 152036 Hom.: 54807 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.925

Gnomad ASJ AF: 0.899

Gnomad EAS AF: 0.994

Gnomad SAS AF: 0.896

Gnomad FIN AF: 0.812

Gnomad MID AF: 0.924

Gnomad NFE AF: 0.900

Gnomad OTH AF: 0.870

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

GnomAD4 genome AF: 0.843 AC: 128221 AN: 152154 Hom.: 54836 Cov.: 32 AF XY: 0.844 AC XY: 62800 AN XY: 74374

African (AFR) AF: 0.691 AC: 28656 AN: 41478

American (AMR) AF: 0.925 AC: 14152 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.899 AC: 3121 AN: 3472

East Asian (EAS) AF: 0.994 AC: 5150 AN: 5180

South Asian (SAS) AF: 0.895 AC: 4317 AN: 4822

European-Finnish (FIN) AF: 0.812 AC: 8601 AN: 10586

Middle Eastern (MID) AF: 0.925 AC: 272 AN: 294

European-Non Finnish (NFE) AF: 0.900 AC: 61216 AN: 68000

Other (OTH) AF: 0.872 AC: 1836 AN: 2106

Alfa AF: 0.886 Hom.: 37554

Bravo AF: 0.845

Asia WGS AF: 0.922 AC: 3206 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.99
DANN	Benign	0.18
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs1796415; hg19: chr12-121543011;