rs10801152

chr1-192792174-A-T

Variant summary

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

The ENST00000644134.1(ENSG00000285280):n.105-25980T>A 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 0.311 in 152,074 control chromosomes in the GnomAD database, including 7,511 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 0.31 (7511 hom., cov: 32)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENST00000644134.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.233

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 (EAS) allele frequency at 95% confidence interval = 0.485 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105371665	XR_922383.2	n.225+125T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000644134.1	n.105-25980T>A		intron_variant, non_coding_transcript_variant
	ENST00000644058.1	n.194-25980T>A		intron_variant, non_coding_transcript_variant
	ENST00000645822.1	n.369+125T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.311 AC: 47314 AN: 151954 Hom.: 7511 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.332

Gnomad ASJ AF: 0.313

Gnomad EAS AF: 0.501

Gnomad SAS AF: 0.281

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.284

Gnomad OTH AF: 0.300

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.311 AC: 47325 AN: 152072 Hom.: 7511 Cov.: 32 AF XY: 0.311 AC XY: 23149 AN XY: 74332

Gnomad4 AFR AF: 0.336

Gnomad4 AMR AF: 0.332

Gnomad4 ASJ AF: 0.313

Gnomad4 EAS AF: 0.501

Gnomad4 SAS AF: 0.279

Gnomad4 FIN AF: 0.272

Gnomad4 NFE AF: 0.284

Gnomad4 OTH AF: 0.303

Alfa AF: 0.289 Hom.: 830

Bravo AF: 0.317

Asia WGS AF: 0.409 AC: 1417 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.83
Dann	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10801152; hg19: chr1-192761304;