chr7-155065627-C-T

Variant names:

• chr7-155065627-C-T
• rs1440454

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 0.49 in 152,006 control chromosomes in the GnomAD database, including 20,586 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 0.49 (20586 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.468
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.631 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.490 AC: 74455 AN: 151888 Hom.: 20587 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.586

Gnomad AMR AF: 0.548

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.518

Gnomad FIN AF: 0.523

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.636

Gnomad OTH AF: 0.513

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

GnomAD4 genome AF: 0.490 AC: 74465 AN: 152006 Hom.: 20586 Cov.: 32 AF XY: 0.484 AC XY: 35984 AN XY: 74290

African (AFR) AF: 0.231 AC: 9574 AN: 41472

American (AMR) AF: 0.549 AC: 8381 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3470

East Asian (EAS) AF: 0.254 AC: 1304 AN: 5142

South Asian (SAS) AF: 0.520 AC: 2500 AN: 4812

European-Finnish (FIN) AF: 0.523 AC: 5523 AN: 10558

Middle Eastern (MID) AF: 0.565 AC: 166 AN: 294

European-Non Finnish (NFE) AF: 0.636 AC: 43239 AN: 67960

Other (OTH) AF: 0.508 AC: 1073 AN: 2112

Alfa AF: 0.581 Hom.: 72735

Bravo AF: 0.481

Asia WGS AF: 0.371 AC: 1290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.7
DANN	Benign	0.75
PhyloP100		0.47

Splicing

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

Other links and lift over

dbSNP: rs1440454; hg19: chr7-154857337;