rs1742848

Variant names:

• chr1-118657073-C-T
• rs1742848

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.402

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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;