rs1037143

Variant names:

• chr1-159598023-T-C
• rs1037143

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.488 AC: 20226 AN: 41422

American (AMR) AF: 0.563 AC: 8594 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1946 AN: 3468

East Asian (EAS) AF: 0.151 AC: 782 AN: 5180

South Asian (SAS) AF: 0.471 AC: 2271 AN: 4820

European-Finnish (FIN) AF: 0.548 AC: 5776 AN: 10536

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.587 AC: 39927 AN: 67974

Other (OTH) AF: 0.574 AC: 1213 AN: 2112

Alfa AF: 0.569 Hom.: 77198

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
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs1037143; hg19: chr1-159567813;