1-43043034-C-T

Variant names:

• chr1-43043034-C-T
• rs841396

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 0.103 in 152,218 control chromosomes in the GnomAD database, including 1,590 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 0.10 (1590 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.943
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.277 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: 0.103 AC: 15705 AN: 152100 Hom.: 1585 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.0883

Gnomad ASJ AF: 0.0449

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.0172

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.0250

Gnomad OTH AF: 0.0772

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

GnomAD4 genome AF: 0.103 AC: 15727 AN: 152218 Hom.: 1590 Cov.: 32 AF XY: 0.103 AC XY: 7690 AN XY: 74434

African (AFR) AF: 0.238 AC: 9888 AN: 41494

American (AMR) AF: 0.0884 AC: 1352 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.0449 AC: 156 AN: 3472

East Asian (EAS) AF: 0.289 AC: 1499 AN: 5178

South Asian (SAS) AF: 0.145 AC: 700 AN: 4822

European-Finnish (FIN) AF: 0.0172 AC: 183 AN: 10622

Middle Eastern (MID) AF: 0.0612 AC: 18 AN: 294

European-Non Finnish (NFE) AF: 0.0249 AC: 1697 AN: 68020

Other (OTH) AF: 0.0769 AC: 162 AN: 2108

Alfa AF: 0.0528 Hom.: 214

Bravo AF: 0.115

Asia WGS AF: 0.210 AC: 731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.45
DANN	Benign	0.17
PhyloP100		-0.94

Splicing

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

Other links and lift over

dbSNP: rs841396; hg19: chr1-43508705;