ENST00000839810.1:n.129+19709G>A

Variant names:

• chr18-49001695-C-T
• rs736839
• ENST00000839810.1:n.129+19709G>A

Variant summary

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

The ENST00000839810.1(ENSG00000309250):​n.129+19709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.28 in 152,104 control chromosomes in the GnomAD database, including 6,383 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 (6383 hom., cov: 33)
• Consequence: ENSG00000309250 ENST00000839810.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0430
• Publications: 6 publications found

Genes affected

ENSG00000309250 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.514 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839810.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309250	ENST00000839810.1		n.129+19709G>A		intron	N/A
	ENSG00000309250	ENST00000839811.1		n.129+19709G>A		intron	N/A
	ENSG00000309250	ENST00000839812.1		n.294-5902G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.280 AC: 42579 AN: 151986 Hom.: 6380 Cov.: 33

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.295

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.243

Gnomad EAS AF: 0.530

Gnomad SAS AF: 0.321

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.269

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

GnomAD4 genome AF: 0.280 AC: 42609 AN: 152104 Hom.: 6383 Cov.: 33 AF XY: 0.286 AC XY: 21261 AN XY: 74330

African (AFR) AF: 0.187 AC: 7775 AN: 41492

American (AMR) AF: 0.341 AC: 5219 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.243 AC: 842 AN: 3472

East Asian (EAS) AF: 0.531 AC: 2736 AN: 5156

South Asian (SAS) AF: 0.322 AC: 1551 AN: 4822

European-Finnish (FIN) AF: 0.311 AC: 3292 AN: 10586

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20312 AN: 67968

Other (OTH) AF: 0.267 AC: 564 AN: 2114

Alfa AF: 0.291 Hom.: 20862

Bravo AF: 0.278

Asia WGS AF: 0.391 AC: 1359 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	6.9
DANN	Benign	0.82
PhyloP100		0.043

Splicing

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

Other links and lift over

dbSNP: rs736839; hg19: chr18-46528065;