chr10-64059007-C-T

Variant names:

• chr10-64059007-C-T
• rs10491075
• ENST00000654191.1:n.517-1119C>T

Variant summary

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

The ENST00000654191.1(ENSG00000228566):​n.517-1119C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0633 in 152,208 control chromosomes in the GnomAD database, including 606 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 0.063 (606 hom., cov: 32)
• Consequence: ENSG00000228566 ENST00000654191.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124902439	XR_007062160.1	n.496-1119C>T		intron_variant	Intron 2 of 5
LOC124902439	XR_007062161.1	n.498-1119C>T		intron_variant	Intron 2 of 5
LOC124902439	XR_007062163.1	n.175-1119C>T		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000228566	ENST00000654191.1	n.517-1119C>T		intron_variant	Intron 2 of 5
ENSG00000228566	ENST00000660795.1	n.266-1119C>T		intron_variant	Intron 2 of 6
ENSG00000228566	ENST00000764129.1	n.211-1119C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0632 AC: 9607 AN: 152090 Hom.: 603 Cov.: 32

Gnomad AFR AF: 0.158

Gnomad AMI AF: 0.0329

Gnomad AMR AF: 0.0588

Gnomad ASJ AF: 0.0498

Gnomad EAS AF: 0.0256

Gnomad SAS AF: 0.0319

Gnomad FIN AF: 0.00528

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0214

Gnomad OTH AF: 0.0616

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

GnomAD4 genome AF: 0.0633 AC: 9639 AN: 152208 Hom.: 606 Cov.: 32 AF XY: 0.0613 AC XY: 4560 AN XY: 74424

African (AFR) AF: 0.159 AC: 6586 AN: 41512

American (AMR) AF: 0.0591 AC: 903 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0498 AC: 173 AN: 3472

East Asian (EAS) AF: 0.0259 AC: 134 AN: 5180

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4826

European-Finnish (FIN) AF: 0.00528 AC: 56 AN: 10614

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0214 AC: 1455 AN: 67992

Other (OTH) AF: 0.0614 AC: 130 AN: 2116

Alfa AF: 0.0334 Hom.: 119

Bravo AF: 0.0733

Asia WGS AF: 0.0420 AC: 145 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.59
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs10491075; hg19: chr10-65818767;