ENST00000735578.1:n.116-1972T>C

Variant names:

• chr19-39241264-T-C
• rs12982533
• ENST00000735578.1:n.116-1972T>C

Variant summary

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

The ENST00000735578.1(ENSG00000296032):​n.116-1972T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.317 in 151,856 control chromosomes in the GnomAD database, including 8,013 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 0.32 (8013 hom., cov: 31)
• Consequence: ENSG00000296032 ENST00000735578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.450
• Publications: 9 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.375 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.116-1972T>C		intron_variant	Intron 1 of 1
ENSG00000296032	ENST00000735579.1	n.90-1972T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48103 AN: 151738 Hom.: 8005 Cov.: 31

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.354

Gnomad AMR AF: 0.358

Gnomad ASJ AF: 0.409

Gnomad EAS AF: 0.0867

Gnomad SAS AF: 0.217

Gnomad FIN AF: 0.222

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.317 AC: 48146 AN: 151856 Hom.: 8013 Cov.: 31 AF XY: 0.310 AC XY: 23021 AN XY: 74220

African (AFR) AF: 0.380 AC: 15707 AN: 41382

American (AMR) AF: 0.357 AC: 5454 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.409 AC: 1418 AN: 3470

East Asian (EAS) AF: 0.0871 AC: 449 AN: 5154

South Asian (SAS) AF: 0.218 AC: 1048 AN: 4818

European-Finnish (FIN) AF: 0.222 AC: 2341 AN: 10552

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.304 AC: 20637 AN: 67914

Other (OTH) AF: 0.315 AC: 663 AN: 2106

Alfa AF: 0.323 Hom.: 1001

Bravo AF: 0.333

Asia WGS AF: 0.169 AC: 589 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	4.2
DANN	Benign	0.41
PhyloP100		0.45

Splicing

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

Other links and lift over

dbSNP: rs12982533; hg19: chr19-39731904;