rs10903118

chr1-24968387-T-C

Variant summary

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

The 1-24968387-T-C variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.475 in 152,018 control chromosomes in the GnomAD database, including 18,534 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 0.48 (18533 hom., cov: 31)
  • Exomes 𝑓: 0.50 (1 hom.)
• Consequence: ENST00000568143.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.15

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000568143.1			downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.475 AC: 72219 AN: 151896 Hom.: 18506 Cov.: 31

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.691

Gnomad AMR AF: 0.639

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.708

Gnomad SAS AF: 0.671

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.500

Gnomad OTH AF: 0.508

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 1 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

Gnomad4 NFE exome AF: 1.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.475 AC: 72266 AN: 152014 Hom.: 18533 Cov.: 31 AF XY: 0.491 AC XY: 36453 AN XY: 74306

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.640

Gnomad4 ASJ AF: 0.509

Gnomad4 EAS AF: 0.707

Gnomad4 SAS AF: 0.671

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.500

Gnomad4 OTH AF: 0.514

Alfa AF: 0.505 Hom.: 27416

Bravo AF: 0.473

Asia WGS AF: 0.692 AC: 2405 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
Cadd	Benign	0.23
Dann	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10903118; hg19: chr1-25294878;