rs1321130

Variant names:

• chr1-231108655-T-C
• rs1321130

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.384 in 152,036 control chromosomes in the GnomAD database, including 12,805 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 0.38 (12805 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.689
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.595 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: 0.384 AC: 58276 AN: 151918 Hom.: 12768 Cov.: 32

Gnomad AFR AF: 0.567

Gnomad AMI AF: 0.398

Gnomad AMR AF: 0.270

Gnomad ASJ AF: 0.284

Gnomad EAS AF: 0.613

Gnomad SAS AF: 0.578

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.384 AC: 58376 AN: 152036 Hom.: 12805 Cov.: 32 AF XY: 0.391 AC XY: 29074 AN XY: 74292

African (AFR) AF: 0.568 AC: 23554 AN: 41482

American (AMR) AF: 0.271 AC: 4133 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.284 AC: 985 AN: 3470

East Asian (EAS) AF: 0.613 AC: 3161 AN: 5156

South Asian (SAS) AF: 0.578 AC: 2783 AN: 4814

European-Finnish (FIN) AF: 0.366 AC: 3870 AN: 10568

Middle Eastern (MID) AF: 0.395 AC: 116 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18669 AN: 67956

Other (OTH) AF: 0.351 AC: 742 AN: 2114

Alfa AF: 0.302 Hom.: 11116

Bravo AF: 0.380

Asia WGS AF: 0.596 AC: 2070 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.45
DANN	Benign	0.60
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs1321130; hg19: chr1-231244401;