rs1079181

Variant names:

• chr1-47712255-T-C
• rs1079181

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 0.0313 in 152,294 control chromosomes in the GnomAD database, including 101 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 0.031 (101 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.155
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.107 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: 0.0313 AC: 4767 AN: 152176 Hom.: 102 Cov.: 33

Gnomad AFR AF: 0.0215

Gnomad AMI AF: 0.0779

Gnomad AMR AF: 0.0274

Gnomad ASJ AF: 0.0580

Gnomad EAS AF: 0.115

Gnomad SAS AF: 0.0391

Gnomad FIN AF: 0.0348

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0286

Gnomad OTH AF: 0.0306

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

GnomAD4 genome AF: 0.0313 AC: 4766 AN: 152294 Hom.: 101 Cov.: 33 AF XY: 0.0325 AC XY: 2422 AN XY: 74468

African (AFR) AF: 0.0215 AC: 894 AN: 41572

American (AMR) AF: 0.0274 AC: 419 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0580 AC: 201 AN: 3468

East Asian (EAS) AF: 0.115 AC: 595 AN: 5168

South Asian (SAS) AF: 0.0386 AC: 186 AN: 4824

European-Finnish (FIN) AF: 0.0348 AC: 370 AN: 10618

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0286 AC: 1948 AN: 68020

Other (OTH) AF: 0.0307 AC: 65 AN: 2116

Alfa AF: 0.0331 Hom.: 54

Bravo AF: 0.0300

Asia WGS AF: 0.0720 AC: 249 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1079181; hg19: chr1-48177927;