rs1440458

Positions:

• chr7-155062444-G-A

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 0.824 in 152,076 control chromosomes in the GnomAD database, including 53,540 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 0.82 (53540 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.56

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 (NFE) allele frequency at 95% confidence interval = 0.941 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: 0.824 AC: 125199 AN: 151958 Hom.: 53521 Cov.: 31

Gnomad AFR AF: 0.584

Gnomad AMI AF: 0.898

Gnomad AMR AF: 0.865

Gnomad ASJ AF: 0.923

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.905

Gnomad FIN AF: 0.917

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.947

Gnomad OTH AF: 0.848

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

GnomAD4 genome AF: 0.824 AC: 125258 AN: 152076 Hom.: 53540 Cov.: 31 AF XY: 0.822 AC XY: 61128 AN XY: 74364

Gnomad4 AFR AF: 0.584

Gnomad4 AMR AF: 0.865

Gnomad4 ASJ AF: 0.923

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.906

Gnomad4 FIN AF: 0.917

Gnomad4 NFE AF: 0.947

Gnomad4 OTH AF: 0.848

Alfa AF: 0.874 Hom.: 9378

Bravo AF: 0.808

Asia WGS AF: 0.787 AC: 2736 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.18
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1440458; hg19: chr7-154854154; COSMIC: COSV67519232;