rs10509193

Variant names:

• chr10-63678259-T-C
• rs10509193
• ENST00000444770.1:n.110-6663T>C

Variant summary

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

The ENST00000444770.1(ENSG00000228566):​n.110-6663T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0676 in 152,292 control chromosomes in the GnomAD database, including 689 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 0.068 (689 hom., cov: 32)
• Consequence: ENSG00000228566 ENST00000444770.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.433
• Publications: 1 publications found

Genes affected

ENSG00000228566 (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 (AFR) allele frequency at 95% confidence interval = 0.169 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000444770.1. 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
	ENSG00000228566	ENST00000444770.1	TSL:3	n.110-6663T>C		intron	N/A
	ENSG00000228566	ENST00000823903.1		n.117-6663T>C		intron	N/A
	ENSG00000228566	ENST00000823904.1		n.98-6663T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0674 AC: 10257 AN: 152174 Hom.: 683 Cov.: 32

Gnomad AFR AF: 0.172

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0337

Gnomad ASJ AF: 0.0277

Gnomad EAS AF: 0.0308

Gnomad SAS AF: 0.0313

Gnomad FIN AF: 0.0225

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0272

Gnomad OTH AF: 0.0478

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

GnomAD4 genome AF: 0.0676 AC: 10298 AN: 152292 Hom.: 689 Cov.: 32 AF XY: 0.0651 AC XY: 4851 AN XY: 74466

African (AFR) AF: 0.173 AC: 7173 AN: 41534

American (AMR) AF: 0.0336 AC: 514 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.0277 AC: 96 AN: 3470

East Asian (EAS) AF: 0.0306 AC: 159 AN: 5190

South Asian (SAS) AF: 0.0313 AC: 151 AN: 4824

European-Finnish (FIN) AF: 0.0225 AC: 239 AN: 10616

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0271 AC: 1847 AN: 68036

Other (OTH) AF: 0.0482 AC: 102 AN: 2116

Alfa AF: 0.0527 Hom.: 65

Bravo AF: 0.0727

Asia WGS AF: 0.0340 AC: 117 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	2.6
DANN	Benign	0.69
PhyloP100		-0.43
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs10509193; hg19: chr10-65438019;