rs10035888

Variant names:

• chr5-36348846-G-A
• rs10035888
• ENST00000756147.1:n.340-1886G>A

Variant summary

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

The ENST00000756147.1(ENSG00000298515):​n.340-1886G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.399 in 151,778 control chromosomes in the GnomAD database, including 12,846 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 0.40 (12846 hom., cov: 30)
• Consequence: ENSG00000298515 ENST00000756147.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0800
• Publications: 1 publications found

Genes affected

ENSG00000298515 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000756147.1. 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
	ENSG00000298515	ENST00000756147.1		n.340-1886G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.399 AC: 60515 AN: 151660 Hom.: 12848 Cov.: 30

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.447

Gnomad AMR AF: 0.375

Gnomad ASJ AF: 0.444

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.244

Gnomad FIN AF: 0.500

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.406

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

GnomAD4 genome AF: 0.399 AC: 60528 AN: 151778 Hom.: 12846 Cov.: 30 AF XY: 0.395 AC XY: 29284 AN XY: 74164

African (AFR) AF: 0.310 AC: 12834 AN: 41368

American (AMR) AF: 0.374 AC: 5700 AN: 15232

Ashkenazi Jewish (ASJ) AF: 0.444 AC: 1538 AN: 3466

East Asian (EAS) AF: 0.0945 AC: 487 AN: 5156

South Asian (SAS) AF: 0.246 AC: 1183 AN: 4818

European-Finnish (FIN) AF: 0.500 AC: 5252 AN: 10502

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32154 AN: 67926

Other (OTH) AF: 0.402 AC: 847 AN: 2106

Alfa AF: 0.441 Hom.: 1943

Bravo AF: 0.384

Asia WGS AF: 0.180 AC: 630 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.1
DANN	Benign	0.27
PhyloP100		-0.080

Splicing

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

Other links and lift over

dbSNP: rs10035888; hg19: chr5-36348948;