rs12972991

Variant names:

• chr19-39241107-A-C
• rs12972991
• ENST00000735578.1:n.116-2129A>C

Variant summary

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

The ENST00000735578.1(ENSG00000296032):​n.116-2129A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.195 in 152,126 control chromosomes in the GnomAD database, including 3,335 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 0.20 (3335 hom., cov: 31)
• Consequence: ENSG00000296032 ENST00000735578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.490
• Publications: 15 publications found

Genes affected

ENSG00000296032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.285 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
ENSG00000296032	ENST00000735578.1	n.116-2129A>C		intron_variant	Intron 1 of 1
ENSG00000296032	ENST00000735579.1	n.90-2129A>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.195 AC: 29671 AN: 152010 Hom.: 3336 Cov.: 31

Gnomad AFR AF: 0.105

Gnomad AMI AF: 0.202

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.276

Gnomad EAS AF: 0.0620

Gnomad SAS AF: 0.163

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.247

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.213

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

GnomAD4 genome AF: 0.195 AC: 29678 AN: 152126 Hom.: 3335 Cov.: 31 AF XY: 0.191 AC XY: 14241 AN XY: 74388

African (AFR) AF: 0.105 AC: 4370 AN: 41512

American (AMR) AF: 0.292 AC: 4461 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.276 AC: 956 AN: 3468

East Asian (EAS) AF: 0.0623 AC: 323 AN: 5184

South Asian (SAS) AF: 0.163 AC: 786 AN: 4820

European-Finnish (FIN) AF: 0.172 AC: 1818 AN: 10592

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16266 AN: 67978

Other (OTH) AF: 0.210 AC: 442 AN: 2102

Alfa AF: 0.237 Hom.: 8961

Bravo AF: 0.202

Asia WGS AF: 0.123 AC: 430 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	6.6
DANN	Benign	0.88
PhyloP100		0.49

Splicing

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

Other links and lift over

dbSNP: rs12972991; hg19: chr19-39731747;