rs10159180

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

ENSG00000260460 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564032.1. 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
	ENSG00000260460	ENST00000564032.1	TSL:6	n.679T>C		non_coding_transcript_exon	Exon 1 of 1

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

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AF: 1.00 AC: 2 AN: 2

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.654 AC: 17 AN: 26

Other (OTH) AF: 1.00 AC: 2 AN: 2

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

African (AFR) AF: 0.614 AC: 25441 AN: 41462

American (AMR) AF: 0.512 AC: 7821 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1971 AN: 3468

East Asian (EAS) AF: 0.693 AC: 3584 AN: 5174

South Asian (SAS) AF: 0.733 AC: 3532 AN: 4818

European-Finnish (FIN) AF: 0.389 AC: 4113 AN: 10562

Middle Eastern (MID) AF: 0.524 AC: 154 AN: 294

European-Non Finnish (NFE) AF: 0.511 AC: 34750 AN: 67952

Other (OTH) AF: 0.539 AC: 1140 AN: 2116

Alfa AF: 0.526 Hom.: 75068

Bravo AF: 0.550

Asia WGS AF: 0.705 AC: 2454 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.17
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs10159180; hg19: chr1-156480324;