10-10053380-G-A

Variant names:

• chr10-10053380-G-A
• rs9633774
• ENST00000738164.1:n.195-37288G>A

Variant summary

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

The ENST00000738164.1(ENSG00000296323):​n.195-37288G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 152,150 control chromosomes in the GnomAD database, including 12,875 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 0.41 (12875 hom., cov: 33)
• Consequence: ENSG00000296323 ENST00000738164.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.238
• Publications: 1 publications found

Genes affected

ENSG00000296323 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738164.1. 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
	ENSG00000296323	ENST00000738164.1		n.195-37288G>A		intron	N/A
	ENSG00000296323	ENST00000738165.1		n.222-37288G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61912 AN: 152032 Hom.: 12859 Cov.: 33

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.322

Gnomad ASJ AF: 0.478

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.430

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.403

Gnomad OTH AF: 0.413

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

GnomAD4 genome AF: 0.407 AC: 61965 AN: 152150 Hom.: 12875 Cov.: 33 AF XY: 0.413 AC XY: 30695 AN XY: 74384

African (AFR) AF: 0.403 AC: 16759 AN: 41538

American (AMR) AF: 0.322 AC: 4921 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.478 AC: 1658 AN: 3472

East Asian (EAS) AF: 0.449 AC: 2318 AN: 5166

South Asian (SAS) AF: 0.430 AC: 2074 AN: 4826

European-Finnish (FIN) AF: 0.507 AC: 5356 AN: 10574

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.403 AC: 27402 AN: 67970

Other (OTH) AF: 0.414 AC: 875 AN: 2116

Alfa AF: 0.405 Hom.: 6501

Bravo AF: 0.391

Asia WGS AF: 0.388 AC: 1349 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.3
DANN	Benign	0.55
PhyloP100		0.24

Splicing

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

Other links and lift over

dbSNP: rs9633774; hg19: chr10-10095343;