chr19-39238839-G-A

Variant names:

• chr19-39238839-G-A
• rs955155
• ENST00000735578.1:n.116-4397G>A

Variant summary

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

The ENST00000735578.1(ENSG00000296032):​n.116-4397G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.197 in 152,188 control chromosomes in the GnomAD database, including 3,556 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 (3556 hom., cov: 32)
• Consequence: ENSG00000296032 ENST00000735578.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.432

Genes affected

ENSG00000296032 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.284 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.116-4397G>A		intron_variant	Intron 1 of 1
ENSG00000296032	ENST00000735579.1	n.90-4397G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.197 AC: 29922 AN: 152070 Hom.: 3557 Cov.: 32

Gnomad AFR AF: 0.0811

Gnomad AMI AF: 0.253

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.278

Gnomad EAS AF: 0.0624

Gnomad SAS AF: 0.193

Gnomad FIN AF: 0.232

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.197 AC: 29929 AN: 152188 Hom.: 3556 Cov.: 32 AF XY: 0.196 AC XY: 14574 AN XY: 74380

African (AFR) AF: 0.0810 AC: 3365 AN: 41540

American (AMR) AF: 0.291 AC: 4450 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.278 AC: 966 AN: 3470

East Asian (EAS) AF: 0.0627 AC: 325 AN: 5182

South Asian (SAS) AF: 0.194 AC: 935 AN: 4824

European-Finnish (FIN) AF: 0.232 AC: 2462 AN: 10590

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16678 AN: 67994

Other (OTH) AF: 0.215 AC: 455 AN: 2114

Alfa AF: 0.240 Hom.: 5811

Bravo AF: 0.198

Asia WGS AF: 0.128 AC: 448 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	11
DANN	Benign	0.79
PhyloP100		0.43

Splicing

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

Publications

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Other links and lift over

dbSNP: rs955155; hg19: chr19-39729479;