chr5-154606753-G-C

Variant names:

• chr5-154606753-G-C
• rs1824935

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 0.352 in 151,998 control chromosomes in the GnomAD database, including 9,813 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 0.35 (9813 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.707
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.386 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: 0.353 AC: 53546 AN: 151880 Hom.: 9812 Cov.: 32

Gnomad AFR AF: 0.284

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.413

Gnomad EAS AF: 0.358

Gnomad SAS AF: 0.315

Gnomad FIN AF: 0.460

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.390

Gnomad OTH AF: 0.391

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

GnomAD4 genome AF: 0.352 AC: 53560 AN: 151998 Hom.: 9813 Cov.: 32 AF XY: 0.353 AC XY: 26207 AN XY: 74268

African (AFR) AF: 0.284 AC: 11766 AN: 41450

American (AMR) AF: 0.288 AC: 4403 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.413 AC: 1433 AN: 3470

East Asian (EAS) AF: 0.358 AC: 1848 AN: 5166

South Asian (SAS) AF: 0.314 AC: 1514 AN: 4814

European-Finnish (FIN) AF: 0.460 AC: 4848 AN: 10540

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.390 AC: 26488 AN: 67958

Other (OTH) AF: 0.392 AC: 830 AN: 2116

Alfa AF: 0.369 Hom.: 1328

Bravo AF: 0.335

Asia WGS AF: 0.366 AC: 1273 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.54
DANN	Benign	0.64
PhyloP100		-0.71

Splicing

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

Other links and lift over

dbSNP: rs1824935; hg19: chr5-153986313;