10-90861032-A-G

Variant names:

• chr10-90861032-A-G
• rs6583737
• ENST00000755194.1:n.354-581A>G

Variant summary

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

The ENST00000755194.1(ENSG00000298380):​n.354-581A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.483 in 152,032 control chromosomes in the GnomAD database, including 21,130 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 0.48 (21130 hom., cov: 32)
• Consequence: ENSG00000298380 ENST00000755194.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.49
• Publications: 3 publications found

Genes affected

ENSG00000298380 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.813 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298380	ENST00000755194.1	n.354-581A>G		intron_variant	Intron 2 of 2
ENSG00000298380	ENST00000755195.1	n.225-581A>G		intron_variant	Intron 2 of 2
ENSG00000298380	ENST00000755196.1	n.316-581A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73246 AN: 151914 Hom.: 21080 Cov.: 32

Gnomad AFR AF: 0.820

Gnomad AMI AF: 0.185

Gnomad AMR AF: 0.434

Gnomad ASJ AF: 0.353

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.454

Gnomad FIN AF: 0.290

Gnomad MID AF: 0.452

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.483 AC: 73356 AN: 152032 Hom.: 21130 Cov.: 32 AF XY: 0.480 AC XY: 35628 AN XY: 74302

African (AFR) AF: 0.820 AC: 34016 AN: 41482

American (AMR) AF: 0.434 AC: 6636 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.353 AC: 1222 AN: 3466

East Asian (EAS) AF: 0.438 AC: 2263 AN: 5168

South Asian (SAS) AF: 0.455 AC: 2192 AN: 4822

European-Finnish (FIN) AF: 0.290 AC: 3065 AN: 10556

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.334 AC: 22691 AN: 67932

Other (OTH) AF: 0.459 AC: 972 AN: 2116

Alfa AF: 0.438 Hom.: 2263

Bravo AF: 0.506

Asia WGS AF: 0.443 AC: 1540 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.94
DANN	Benign	0.50
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs6583737; hg19: chr10-92620789;