chr19-39944141-T-C

Variant names:

• chr19-39944141-T-C
• rs2231738
• ENST00000794087.1:n.263-4391T>C

Variant summary

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

The ENST00000794087.1(ENSG00000303389):​n.263-4391T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.277 in 151,944 control chromosomes in the GnomAD database, including 10,841 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 0.28 (10841 hom., cov: 32)
• Consequence: ENSG00000303389 ENST00000794087.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.928
• Publications: 12 publications found

Genes affected

ENSG00000303389 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.673 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
ENSG00000303389	ENST00000794087.1	n.263-4391T>C		intron_variant	Intron 1 of 1
ENSG00000303389	ENST00000794088.1	n.273+1422T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.277 AC: 41992 AN: 151828 Hom.: 10794 Cov.: 32

Gnomad AFR AF: 0.679

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.148

Gnomad ASJ AF: 0.199

Gnomad EAS AF: 0.259

Gnomad SAS AF: 0.213

Gnomad FIN AF: 0.0908

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.104

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.277 AC: 42103 AN: 151944 Hom.: 10841 Cov.: 32 AF XY: 0.275 AC XY: 20404 AN XY: 74266

African (AFR) AF: 0.680 AC: 28171 AN: 41420

American (AMR) AF: 0.148 AC: 2263 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.199 AC: 690 AN: 3472

East Asian (EAS) AF: 0.259 AC: 1334 AN: 5152

South Asian (SAS) AF: 0.213 AC: 1020 AN: 4798

European-Finnish (FIN) AF: 0.0908 AC: 959 AN: 10560

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.104 AC: 7044 AN: 67958

Other (OTH) AF: 0.239 AC: 504 AN: 2106

Alfa AF: 0.160 Hom.: 2527

Bravo AF: 0.297

Asia WGS AF: 0.243 AC: 847 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	4.0
DANN	Benign	0.61
PhyloP100		-0.93

Splicing

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

Other links and lift over

dbSNP: rs2231738; hg19: chr19-40450048;