rs1486155

Positions:

• chr7-46256119-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 0.613 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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.730

Gnomad4 ASJ AF: 0.635

Gnomad4 EAS AF: 0.856

Gnomad4 SAS AF: 0.699

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.604

Gnomad4 OTH AF: 0.643

Alfa AF: 0.602 Hom.: 6138

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1486155; hg19: chr7-46295717;