chr19-39241143-A-G

Variant names:

• chr19-39241143-A-G
• rs12980275
• ENST00000735578.1:n.116-2093A>G

Variant summary

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

The ENST00000735578.1(ENSG00000296032):​n.116-2093A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.355 in 151,908 control chromosomes in the GnomAD database, including 10,661 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 0.36 (10661 hom., cov: 31)
• Consequence: ENSG00000296032 ENST00000735578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 233 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=-1.07).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.513 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000735578.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296032	ENST00000735578.1		n.116-2093A>G		intron	N/A
	ENSG00000296032	ENST00000735579.1		n.90-2093A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.355 AC: 53870 AN: 151790 Hom.: 10634 Cov.: 31

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.370

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.0792

Gnomad SAS AF: 0.216

Gnomad FIN AF: 0.223

Gnomad MID AF: 0.367

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.355 AC: 53945 AN: 151908 Hom.: 10661 Cov.: 31 AF XY: 0.347 AC XY: 25799 AN XY: 74254

African (AFR) AF: 0.518 AC: 21441 AN: 41356

American (AMR) AF: 0.370 AC: 5636 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.403 AC: 1400 AN: 3470

East Asian (EAS) AF: 0.0795 AC: 412 AN: 5180

South Asian (SAS) AF: 0.216 AC: 1039 AN: 4812

European-Finnish (FIN) AF: 0.223 AC: 2356 AN: 10568

Middle Eastern (MID) AF: 0.371 AC: 109 AN: 294

European-Non Finnish (NFE) AF: 0.302 AC: 20544 AN: 67964

Other (OTH) AF: 0.337 AC: 709 AN: 2106

Alfa AF: 0.323 Hom.: 39218

Bravo AF: 0.374

Asia WGS AF: 0.180 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.26
DANN	Benign	0.17
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs12980275; hg19: chr19-39731783;