rs1331046

Variant names:

• chr1-232133407-C-A
• rs1331046

Your query was ambiguous. Multiple possible variants found:

• chr1-232133407-C-A
• chr1-232133407-C-T

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 0.0473 in 152,160 control chromosomes in the GnomAD database, including 262 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 0.047 (262 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.142

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.186 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: 0.0473 AC: 7193 AN: 152042 Hom.: 261 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.177

Gnomad AMR AF: 0.0613

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.195

Gnomad SAS AF: 0.0365

Gnomad FIN AF: 0.0516

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0442

Gnomad OTH AF: 0.0480

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

GnomAD4 genome AF: 0.0473 AC: 7204 AN: 152160 Hom.: 262 Cov.: 32 AF XY: 0.0491 AC XY: 3650 AN XY: 74378

Gnomad4 AFR AF: 0.0277

Gnomad4 AMR AF: 0.0615

Gnomad4 ASJ AF: 0.0314

Gnomad4 EAS AF: 0.196

Gnomad4 SAS AF: 0.0367

Gnomad4 FIN AF: 0.0516

Gnomad4 NFE AF: 0.0442

Gnomad4 OTH AF: 0.0484

Alfa AF: 0.0367 Hom.: 47

Bravo AF: 0.0487

Asia WGS AF: 0.0930 AC: 324 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1331046; hg19: chr1-232269153;