10-34998722-T-G

Variant names:

• chr10-34998722-T-G
• rs17582416
• ENST00000775934.1:n.64-11531T>G

Variant summary

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

The ENST00000775934.1(ENSG00000301061):​n.64-11531T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.307 in 151,912 control chromosomes in the GnomAD database, including 7,450 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 0.31 (7450 hom., cov: 32)
• Consequence: ENSG00000301061 ENST00000775934.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.54
• Publications: 55 publications found

Genes affected

ENSG00000301061 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775934.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301061	ENST00000775934.1		n.64-11531T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.307 AC: 46567 AN: 151792 Hom.: 7434 Cov.: 32

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.305

Gnomad ASJ AF: 0.399

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.345

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.346

Gnomad OTH AF: 0.327

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

GnomAD4 genome AF: 0.307 AC: 46636 AN: 151912 Hom.: 7450 Cov.: 32 AF XY: 0.309 AC XY: 22921 AN XY: 74268

African (AFR) AF: 0.211 AC: 8740 AN: 41432

American (AMR) AF: 0.305 AC: 4657 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.399 AC: 1382 AN: 3466

East Asian (EAS) AF: 0.295 AC: 1519 AN: 5144

South Asian (SAS) AF: 0.346 AC: 1664 AN: 4806

European-Finnish (FIN) AF: 0.390 AC: 4121 AN: 10570

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.346 AC: 23523 AN: 67920

Other (OTH) AF: 0.334 AC: 704 AN: 2108

Alfa AF: 0.332 Hom.: 27184

Bravo AF: 0.295

Asia WGS AF: 0.348 AC: 1208 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.36
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs17582416; hg19: chr10-35287650;