1-3041036-T-C

Position:

• chr1-3041036-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 0.172 in 152,240 control chromosomes in the GnomAD database, including 2,454 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 0.17 (2454 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.392 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: 0.172 AC: 26209 AN: 152122 Hom.: 2454 Cov.: 33

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.143

Gnomad AMR AF: 0.223

Gnomad ASJ AF: 0.108

Gnomad EAS AF: 0.406

Gnomad SAS AF: 0.102

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.176

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.172 AC: 26235 AN: 152240 Hom.: 2454 Cov.: 33 AF XY: 0.171 AC XY: 12707 AN XY: 74430

Gnomad4 AFR AF: 0.145

Gnomad4 AMR AF: 0.223

Gnomad4 ASJ AF: 0.108

Gnomad4 EAS AF: 0.406

Gnomad4 SAS AF: 0.101

Gnomad4 FIN AF: 0.127

Gnomad4 NFE AF: 0.176

Gnomad4 OTH AF: 0.179

Alfa AF: 0.173 Hom.: 541

Bravo AF: 0.184

Asia WGS AF: 0.226 AC: 787 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.092
DANN	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12409277; hg19: chr1-2957600;