rs1934712

Variant names:

• chr1-102488445-G-A
• rs1934712

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 0.432 in 151,798 control chromosomes in the GnomAD database, including 15,996 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 0.43 (15996 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.215

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.533 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: 0.432 AC: 65500 AN: 151680 Hom.: 15993 Cov.: 31

Gnomad AFR AF: 0.182

Gnomad AMI AF: 0.597

Gnomad AMR AF: 0.489

Gnomad ASJ AF: 0.531

Gnomad EAS AF: 0.426

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.538

Gnomad OTH AF: 0.462

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

GnomAD4 genome AF: 0.432 AC: 65519 AN: 151798 Hom.: 15996 Cov.: 31 AF XY: 0.434 AC XY: 32223 AN XY: 74172

Gnomad4 AFR AF: 0.182

Gnomad4 AMR AF: 0.489

Gnomad4 ASJ AF: 0.531

Gnomad4 EAS AF: 0.426

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.538

Gnomad4 OTH AF: 0.465

Alfa AF: 0.481 Hom.: 3545

Bravo AF: 0.414

Asia WGS AF: 0.459 AC: 1593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.8
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1934712; hg19: chr1-102954001;