ENST00000839508.1:n.538-5896G>A

Variant names:

• chr10-29957351-G-A
• rs10508755
• ENST00000839508.1:n.538-5896G>A

Variant summary

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

The ENST00000839508.1(ENSG00000289616):​n.538-5896G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,068 control chromosomes in the GnomAD database, including 2,554 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 0.11 (2554 hom., cov: 33)
• Consequence: ENSG00000289616 ENST00000839508.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.60
• Publications: 1 publications found

Genes affected

ENSG00000289616 (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 (AFR) allele frequency at 95% confidence interval = 0.341 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000839508.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289616	ENST00000839508.1		n.538-5896G>A		intron	N/A
	ENSG00000309221	ENST00000839588.1		n.409+2186C>T		intron	N/A
	ENSG00000309221	ENST00000839589.1		n.409+2186C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16172 AN: 151950 Hom.: 2537 Cov.: 33

Gnomad AFR AF: 0.345

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0442

Gnomad ASJ AF: 0.0297

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0688

Gnomad FIN AF: 0.000850

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.00847

Gnomad OTH AF: 0.0845

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

GnomAD4 genome AF: 0.107 AC: 16227 AN: 152068 Hom.: 2554 Cov.: 33 AF XY: 0.104 AC XY: 7766 AN XY: 74322

African (AFR) AF: 0.345 AC: 14305 AN: 41434

American (AMR) AF: 0.0443 AC: 676 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.0297 AC: 103 AN: 3472

East Asian (EAS) AF: 0.00271 AC: 14 AN: 5172

South Asian (SAS) AF: 0.0680 AC: 327 AN: 4810

European-Finnish (FIN) AF: 0.000850 AC: 9 AN: 10584

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.00848 AC: 577 AN: 68010

Other (OTH) AF: 0.0837 AC: 176 AN: 2104

Alfa AF: 0.0168 Hom.: 39

Bravo AF: 0.120

Asia WGS AF: 0.0480 AC: 167 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	0.98
DANN	Benign	0.59
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs10508755; hg19: chr10-30246280;