rs10159180

Variant names:

• chr1-156510532-T-C
• rs10159180
• ENST00000564032.1:n.679T>C

Variant summary

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

The ENST00000564032.1(ENSG00000260460):​n.679T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 152,058 control chromosomes in the GnomAD database, including 23,113 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 0.55 (23104 hom., cov: 32)
  • Exomes 𝑓: 0.70 (9 hom.)
• Consequence: ENSG00000260460 ENST00000564032.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.552

Genes affected

ENSG00000260460 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.713 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
ENSG00000260460	ENST00000564032.1	n.679T>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82798 AN: 151910 Hom.: 23071 Cov.: 32

Gnomad AFR AF: 0.614

Gnomad AMI AF: 0.408

Gnomad AMR AF: 0.512

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.733

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.519

Gnomad NFE AF: 0.511

Gnomad OTH AF: 0.537

GnomAD4 exome AF: 0.700 AC: 21 AN: 30 Hom.: 9 Cov.: 0 AF XY: 0.650 AC XY: 13 AN XY: 20

Gnomad4 ASJ exome AF: 1.00

Gnomad4 NFE exome AF: 0.654

Gnomad4 OTH exome AF: 1.00

GnomAD4 genome AF: 0.545 AC: 82878 AN: 152028 Hom.: 23104 Cov.: 32 AF XY: 0.541 AC XY: 40228 AN XY: 74302

Gnomad4 AFR AF: 0.614

Gnomad4 AMR AF: 0.512

Gnomad4 ASJ AF: 0.568

Gnomad4 EAS AF: 0.693

Gnomad4 SAS AF: 0.733

Gnomad4 FIN AF: 0.389

Gnomad4 NFE AF: 0.511

Gnomad4 OTH AF: 0.539

Alfa AF: 0.521 Hom.: 33211

Bravo AF: 0.550

Asia WGS AF: 0.705 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.17

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10159180; hg19: chr1-156480324;