chr12-131378358-G-A

Variant names:

• chr12-131378358-G-A
• rs7965445
• ENST00000833340.1:n.629-1501G>A

Variant summary

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

The ENST00000833340.1(ENSG00000308331):​n.629-1501G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 150,066 control chromosomes in the GnomAD database, including 3,456 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 0.17 (3456 hom., cov: 31)
• Consequence: ENSG00000308331 ENST00000833340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.100
• Publications: 8 publications found

Genes affected

ENSG00000308331 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.25).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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
ENSG00000308331	ENST00000833340.1	n.629-1501G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25333 AN: 149942 Hom.: 3450 Cov.: 31

Gnomad AFR AF: 0.387

Gnomad AMI AF: 0.00776

Gnomad AMR AF: 0.0940

Gnomad ASJ AF: 0.0801

Gnomad EAS AF: 0.00120

Gnomad SAS AF: 0.0693

Gnomad FIN AF: 0.0985

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.0911

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.169 AC: 25379 AN: 150066 Hom.: 3456 Cov.: 31 AF XY: 0.165 AC XY: 12085 AN XY: 73380

African (AFR) AF: 0.386 AC: 15842 AN: 40990

American (AMR) AF: 0.0938 AC: 1414 AN: 15076

Ashkenazi Jewish (ASJ) AF: 0.0801 AC: 276 AN: 3444

East Asian (EAS) AF: 0.00120 AC: 6 AN: 4982

South Asian (SAS) AF: 0.0704 AC: 330 AN: 4690

European-Finnish (FIN) AF: 0.0985 AC: 1034 AN: 10502

Middle Eastern (MID) AF: 0.132 AC: 38 AN: 288

European-Non Finnish (NFE) AF: 0.0911 AC: 6117 AN: 67116

Other (OTH) AF: 0.152 AC: 315 AN: 2076

Alfa AF: 0.118 Hom.: 2897

Bravo AF: 0.177

Asia WGS AF: 0.0480 AC: 169 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.3
CADD	Benign	1.4
DANN	Benign	0.53
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs7965445; hg19: chr12-131862903;