rs10491075

chr10-64059007-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000654191.1(ENSG00000228566):n.517-1119C>T variant causes a intron, non coding transcript 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: ENST00000654191.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
LOC124902439	XR_007062161.1	n.498-1119C>T		intron_variant, non_coding_transcript_variant
LOC124902439	XR_007062160.1	n.496-1119C>T		intron_variant, non_coding_transcript_variant
LOC124902439	XR_007062163.1	n.175-1119C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000654191.1	n.517-1119C>T		intron_variant, non_coding_transcript_variant
	ENST00000660795.1	n.266-1119C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0591

Gnomad4 ASJ AF: 0.0498

Gnomad4 EAS AF: 0.0259

Gnomad4 SAS AF: 0.0311

Gnomad4 FIN AF: 0.00528

Gnomad4 NFE AF: 0.0214

Gnomad4 OTH AF: 0.0614

Alfa AF: 0.0324 Hom.: 98

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10491075; hg19: chr10-65818767;