10-3539029-A-G

Variant names:

• chr10-3539029-A-G
• rs10795055
• ENST00000654955.1:n.257-1998T>C

Variant summary

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

The ENST00000654955.1(ENSG00000236892):​n.257-1998T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.537 in 152,044 control chromosomes in the GnomAD database, including 22,694 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 0.54 (22694 hom., cov: 32)
• Consequence: ENSG00000236892 ENST00000654955.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 6 publications found

Genes affected

ENSG00000236892 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.613 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105376360	NR_131187.1	n.163-209659A>G		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000236892	ENST00000654955.1	n.257-1998T>C		intron_variant	Intron 2 of 2
ENSG00000236892	ENST00000736471.1	n.62-1998T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.538 AC: 81667 AN: 151926 Hom.: 22686 Cov.: 32

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.673

Gnomad EAS AF: 0.368

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.618

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.537 AC: 81716 AN: 152044 Hom.: 22694 Cov.: 32 AF XY: 0.535 AC XY: 39760 AN XY: 74310

African (AFR) AF: 0.410 AC: 17014 AN: 41466

American (AMR) AF: 0.529 AC: 8086 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.673 AC: 2331 AN: 3466

East Asian (EAS) AF: 0.368 AC: 1897 AN: 5150

South Asian (SAS) AF: 0.592 AC: 2849 AN: 4810

European-Finnish (FIN) AF: 0.545 AC: 5757 AN: 10562

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.618 AC: 42020 AN: 67984

Other (OTH) AF: 0.557 AC: 1179 AN: 2116

Alfa AF: 0.579 Hom.: 5771

Bravo AF: 0.527

Asia WGS AF: 0.460 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.043
DANN	Benign	0.31
PhyloP100		-0.22

Splicing

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

Other links and lift over

dbSNP: rs10795055; hg19: chr10-3581221;