rs1486140

Variant names:

• chr7-46236039-T-C
• rs1486140

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 0.477 in 146,616 control chromosomes in the GnomAD database, including 18,054 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 0.48 (18054 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.939

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.679 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: 0.477 AC: 69952 AN: 146504 Hom.: 18055 Cov.: 31

Gnomad AFR AF: 0.235

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.549

Gnomad ASJ AF: 0.581

Gnomad EAS AF: 0.699

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.575

Gnomad MID AF: 0.607

Gnomad NFE AF: 0.549

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.477 AC: 69959 AN: 146616 Hom.: 18054 Cov.: 31 AF XY: 0.485 AC XY: 34705 AN XY: 71612

Gnomad4 AFR AF: 0.235

Gnomad4 AMR AF: 0.549

Gnomad4 ASJ AF: 0.581

Gnomad4 EAS AF: 0.698

Gnomad4 SAS AF: 0.537

Gnomad4 FIN AF: 0.575

Gnomad4 NFE AF: 0.549

Gnomad4 OTH AF: 0.534

Alfa AF: 0.464 Hom.: 2586

Bravo AF: 0.446

Asia WGS AF: 0.567 AC: 1973 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	1.2
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1486140; hg19: chr7-46275637;