12-102731912-G-A

Variant names:

• chr12-102731912-G-A
• rs2172873
• ENST00000737486.1:n.312+24540G>A

Variant summary

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

The ENST00000737486.1(ENSG00000296233):​n.312+24540G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.135 in 152,126 control chromosomes in the GnomAD database, including 2,626 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 0.13 (2626 hom., cov: 32)
• Consequence: ENSG00000296233 ENST00000737486.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.937
• Publications: 9 publications found

Genes affected

ENSG00000296233 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.332 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
ENSG00000296233	ENST00000737486.1	n.312+24540G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.134 AC: 20415 AN: 152008 Hom.: 2598 Cov.: 32

Gnomad AFR AF: 0.335

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0743

Gnomad ASJ AF: 0.0784

Gnomad EAS AF: 0.0917

Gnomad SAS AF: 0.0990

Gnomad FIN AF: 0.0301

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0531

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.135 AC: 20493 AN: 152126 Hom.: 2626 Cov.: 32 AF XY: 0.132 AC XY: 9787 AN XY: 74344

African (AFR) AF: 0.336 AC: 13936 AN: 41434

American (AMR) AF: 0.0742 AC: 1135 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0784 AC: 272 AN: 3470

East Asian (EAS) AF: 0.0919 AC: 476 AN: 5178

South Asian (SAS) AF: 0.0985 AC: 475 AN: 4822

European-Finnish (FIN) AF: 0.0301 AC: 319 AN: 10606

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0531 AC: 3609 AN: 68004

Other (OTH) AF: 0.115 AC: 243 AN: 2110

Alfa AF: 0.0783 Hom.: 3814

Bravo AF: 0.145

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.2
DANN	Benign	0.64
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs2172873; hg19: chr12-103125690;