chr12-102972207-C-A

Variant names:

• chr12-102972207-C-A
• rs1391681
• ENST00000737239.1:n.339+7356C>A

Variant summary

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

The ENST00000737239.1(ENSG00000288092):​n.339+7356C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 152,104 control chromosomes in the GnomAD database, including 24,434 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 0.53 (24434 hom., cov: 34)
• Consequence: ENSG00000288092 ENST00000737239.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0420
• Publications: 3 publications found

Genes affected

ENSG00000288092 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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
ENSG00000288092	ENST00000737239.1	n.339+7356C>A		intron_variant	Intron 1 of 2
ENSG00000288092	ENST00000737240.1	n.70+7356C>A		intron_variant	Intron 1 of 3
ENSG00000288092	ENST00000737241.1	n.69+7356C>A		intron_variant	Intron 1 of 3
ENSG00000288092	ENST00000737242.1	n.45+7356C>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80893 AN: 151986 Hom.: 24425 Cov.: 34

Gnomad AFR AF: 0.233

Gnomad AMI AF: 0.641

Gnomad AMR AF: 0.682

Gnomad ASJ AF: 0.577

Gnomad EAS AF: 0.870

Gnomad SAS AF: 0.754

Gnomad FIN AF: 0.681

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.611

Gnomad OTH AF: 0.559

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

GnomAD4 genome AF: 0.532 AC: 80923 AN: 152104 Hom.: 24434 Cov.: 34 AF XY: 0.541 AC XY: 40209 AN XY: 74352

African (AFR) AF: 0.233 AC: 9665 AN: 41480

American (AMR) AF: 0.683 AC: 10433 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.577 AC: 2003 AN: 3470

East Asian (EAS) AF: 0.870 AC: 4510 AN: 5184

South Asian (SAS) AF: 0.753 AC: 3635 AN: 4826

European-Finnish (FIN) AF: 0.681 AC: 7189 AN: 10556

Middle Eastern (MID) AF: 0.613 AC: 179 AN: 292

European-Non Finnish (NFE) AF: 0.611 AC: 41539 AN: 67994

Other (OTH) AF: 0.563 AC: 1188 AN: 2110

Alfa AF: 0.589 Hom.: 5172

Bravo AF: 0.515

Asia WGS AF: 0.775 AC: 2694 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.53
PhyloP100		0.042

Splicing

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

Other links and lift over

dbSNP: rs1391681; hg19: chr12-103365985;