rs1440458

Variant names:

• chr7-155062444-G-A
• rs1440458

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 0.824 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
• Publications: 0 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 (NFE) allele frequency at 95% confidence interval = 0.941 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: 0.824 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

African (AFR) AF: 0.584 AC: 24174 AN: 41394

American (AMR) AF: 0.865 AC: 13215 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.923 AC: 3203 AN: 3472

East Asian (EAS) AF: 0.628 AC: 3242 AN: 5162

South Asian (SAS) AF: 0.906 AC: 4367 AN: 4820

European-Finnish (FIN) AF: 0.917 AC: 9729 AN: 10606

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.947 AC: 64448 AN: 68024

Other (OTH) AF: 0.848 AC: 1793 AN: 2114

Alfa AF: 0.866 Hom.: 9512

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
PhyloP100		-1.6

Splicing

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

Other links and lift over

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