10-64688715-T-C

Variant names:

• chr10-64688715-T-C
• rs7900909
• ENST00000654191.1:n.734-2727T>C

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.734-2727T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,984 control chromosomes in the GnomAD database, including 3,194 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 0.20 (3194 hom., cov: 32)
• Consequence: ENSG00000228566 ENST00000654191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.162
• Publications: 7 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=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000654191.1. 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
	ENSG00000228566	ENST00000654191.1		n.734-2727T>C		intron	N/A
	ENSG00000228566	ENST00000660795.1		n.580-2727T>C		intron	N/A
	ENSG00000228566	ENST00000821348.1		n.83-2727T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30005 AN: 151866 Hom.: 3178 Cov.: 32

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.256

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.225

Gnomad EAS AF: 0.345

Gnomad SAS AF: 0.260

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.129

Gnomad NFE AF: 0.145

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.198 AC: 30041 AN: 151984 Hom.: 3194 Cov.: 32 AF XY: 0.203 AC XY: 15058 AN XY: 74260

African (AFR) AF: 0.224 AC: 9289 AN: 41478

American (AMR) AF: 0.285 AC: 4345 AN: 15242

Ashkenazi Jewish (ASJ) AF: 0.225 AC: 782 AN: 3472

East Asian (EAS) AF: 0.345 AC: 1777 AN: 5154

South Asian (SAS) AF: 0.259 AC: 1248 AN: 4826

European-Finnish (FIN) AF: 0.197 AC: 2080 AN: 10570

Middle Eastern (MID) AF: 0.139 AC: 40 AN: 288

European-Non Finnish (NFE) AF: 0.145 AC: 9867 AN: 67940

Other (OTH) AF: 0.181 AC: 381 AN: 2106

Alfa AF: 0.173 Hom.: 2810

Bravo AF: 0.208

Asia WGS AF: 0.276 AC: 950 AN: 3450

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	6.5
DANN	Benign	0.77
PhyloP100		0.16

Splicing

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

Other links and lift over

dbSNP: rs7900909; hg19: chr10-66448472;