rs1486155

Variant names:

• chr7-46256119-C-T
• rs1486155

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 0.613 in 151,982 control chromosomes in the GnomAD database, including 28,991 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 0.61 (28991 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.835 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: 0.613 AC: 93043 AN: 151864 Hom.: 28971 Cov.: 32

Gnomad AFR AF: 0.540

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.729

Gnomad ASJ AF: 0.635

Gnomad EAS AF: 0.857

Gnomad SAS AF: 0.700

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.604

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.613 AC: 93101 AN: 151982 Hom.: 28991 Cov.: 32 AF XY: 0.620 AC XY: 46059 AN XY: 74290

African (AFR) AF: 0.540 AC: 22376 AN: 41436

American (AMR) AF: 0.730 AC: 11147 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.635 AC: 2203 AN: 3468

East Asian (EAS) AF: 0.856 AC: 4431 AN: 5174

South Asian (SAS) AF: 0.699 AC: 3375 AN: 4826

European-Finnish (FIN) AF: 0.599 AC: 6334 AN: 10566

Middle Eastern (MID) AF: 0.680 AC: 200 AN: 294

European-Non Finnish (NFE) AF: 0.604 AC: 41021 AN: 67920

Other (OTH) AF: 0.643 AC: 1358 AN: 2112

Alfa AF: 0.603 Hom.: 10171

Bravo AF: 0.621

Asia WGS AF: 0.739 AC: 2564 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.42
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs1486155; hg19: chr7-46295717;