1-104678343-C-T

Variant names:

• chr1-104678343-C-T
• rs12725071

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 0.0543 in 151,618 control chromosomes in the GnomAD database, including 305 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 0.054 (305 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.214

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0802 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: 0.0543 AC: 8224 AN: 151500 Hom.: 305 Cov.: 32

Gnomad AFR AF: 0.0144

Gnomad AMI AF: 0.139

Gnomad AMR AF: 0.0424

Gnomad ASJ AF: 0.0240

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0137

Gnomad FIN AF: 0.102

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0385

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

GnomAD4 genome AF: 0.0543 AC: 8227 AN: 151618 Hom.: 305 Cov.: 32 AF XY: 0.0546 AC XY: 4043 AN XY: 74082

Gnomad4 AFR AF: 0.0144

Gnomad4 AMR AF: 0.0423

Gnomad4 ASJ AF: 0.0240

Gnomad4 EAS AF: 0.000964

Gnomad4 SAS AF: 0.0137

Gnomad4 FIN AF: 0.102

Gnomad4 NFE AF: 0.0820

Gnomad4 OTH AF: 0.0381

Alfa AF: 0.0648 Hom.: 211

Bravo AF: 0.0484

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.3
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12725071; hg19: chr1-105220965;