1-152065039-T-C

Variant names:

• chr1-152065039-T-C
• rs3124314

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 0.527 in 152,058 control chromosomes in the GnomAD database, including 21,897 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 0.53 (21897 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.135

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.726 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: 0.527 AC: 80065 AN: 151940 Hom.: 21850 Cov.: 31

Gnomad AFR AF: 0.621

Gnomad AMI AF: 0.538

Gnomad AMR AF: 0.603

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.619

Gnomad SAS AF: 0.748

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.446

Gnomad OTH AF: 0.520

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

GnomAD4 genome AF: 0.527 AC: 80161 AN: 152058 Hom.: 21897 Cov.: 31 AF XY: 0.530 AC XY: 39401 AN XY: 74320

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.604

Gnomad4 ASJ AF: 0.642

Gnomad4 EAS AF: 0.619

Gnomad4 SAS AF: 0.746

Gnomad4 FIN AF: 0.382

Gnomad4 NFE AF: 0.446

Gnomad4 OTH AF: 0.517

Alfa AF: 0.470 Hom.: 20799

Bravo AF: 0.546

Asia WGS AF: 0.694 AC: 2410 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	2.8
DANN	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3124314; hg19: chr1-152037515;