chr4-154527912-T-A

Variant names:

• chr4-154527912-T-A
• rs13123551

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 0.525 in 152,018 control chromosomes in the GnomAD database, including 21,203 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 0.52 (21203 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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: 0.525 AC: 79690 AN: 151900 Hom.: 21191 Cov.: 32

Gnomad AFR AF: 0.507

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.458

Gnomad ASJ AF: 0.509

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.604

Gnomad FIN AF: 0.515

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.525 AC: 79735 AN: 152018 Hom.: 21203 Cov.: 32 AF XY: 0.525 AC XY: 39010 AN XY: 74288

African (AFR) AF: 0.507 AC: 21009 AN: 41446

American (AMR) AF: 0.457 AC: 6991 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.509 AC: 1767 AN: 3470

East Asian (EAS) AF: 0.692 AC: 3575 AN: 5168

South Asian (SAS) AF: 0.603 AC: 2904 AN: 4816

European-Finnish (FIN) AF: 0.515 AC: 5433 AN: 10544

Middle Eastern (MID) AF: 0.534 AC: 157 AN: 294

European-Non Finnish (NFE) AF: 0.535 AC: 36338 AN: 67976

Other (OTH) AF: 0.531 AC: 1119 AN: 2106

Alfa AF: 0.529 Hom.: 2045

Bravo AF: 0.519

Asia WGS AF: 0.635 AC: 2203 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.13
DANN	Benign	0.086
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs13123551; hg19: chr4-155449064;