rs1486140

Positions:

• chr7-46236039-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;