rs1037143

Positions:

• chr1-159598023-T-C

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 0.536 in 151,994 control chromosomes in the GnomAD database, including 22,459 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 0.54 (22459 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.46

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 (NFE) allele frequency at 95% confidence interval = 0.583 is higher than 0.05.

Transcripts

RefSeq

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

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81429 AN: 151876 Hom.: 22440 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.563

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.151

Gnomad SAS AF: 0.471

Gnomad FIN AF: 0.548

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.587

Gnomad OTH AF: 0.576

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

GnomAD4 genome AF: 0.536 AC: 81496 AN: 151994 Hom.: 22459 Cov.: 32 AF XY: 0.531 AC XY: 39466 AN XY: 74276

Gnomad4 AFR AF: 0.488

Gnomad4 AMR AF: 0.563

Gnomad4 ASJ AF: 0.561

Gnomad4 EAS AF: 0.151

Gnomad4 SAS AF: 0.471

Gnomad4 FIN AF: 0.548

Gnomad4 NFE AF: 0.587

Gnomad4 OTH AF: 0.574

Alfa AF: 0.582 Hom.: 31615

Bravo AF: 0.535

Asia WGS AF: 0.305 AC: 1064 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.73
DANN	Benign	0.69

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1037143; hg19: chr1-159567813;