rs1742848

Positions:

• chr1-118657073-C-T

Variant summary

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

The variant allele was found at a frequency of 0.532 in 151,520 control chromosomes in the GnomAD database, including 23,592 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 0.53 (23592 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.647 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.118657073C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.532 AC: 80568 AN: 151404 Hom.: 23589 Cov.: 31

Gnomad AFR AF: 0.272

Gnomad AMI AF: 0.653

Gnomad AMR AF: 0.599

Gnomad ASJ AF: 0.636

Gnomad EAS AF: 0.425

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.698

Gnomad NFE AF: 0.652

Gnomad OTH AF: 0.572

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.532 AC: 80584 AN: 151520 Hom.: 23592 Cov.: 31 AF XY: 0.533 AC XY: 39481 AN XY: 74022

Gnomad4 AFR AF: 0.272

Gnomad4 AMR AF: 0.599

Gnomad4 ASJ AF: 0.636

Gnomad4 EAS AF: 0.424

Gnomad4 SAS AF: 0.587

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.652

Gnomad4 OTH AF: 0.572

Alfa AF: 0.619 Hom.: 16745

Bravo AF: 0.516

Asia WGS AF: 0.503 AC: 1732 AN: 3448

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.23
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1742848; hg19: chr1-119199696;