chr5-154606484-C-T

Variant names:

• chr5-154606484-C-T
• rs1824936

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 0.389 in 151,940 control chromosomes in the GnomAD database, including 11,726 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 0.39 (11726 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.138
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 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: 0.389 AC: 59068 AN: 151822 Hom.: 11721 Cov.: 31

Gnomad AFR AF: 0.404

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.466

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.391

Gnomad OTH AF: 0.415

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

GnomAD4 genome AF: 0.389 AC: 59096 AN: 151940 Hom.: 11726 Cov.: 31 AF XY: 0.389 AC XY: 28854 AN XY: 74256

African (AFR) AF: 0.404 AC: 16715 AN: 41424

American (AMR) AF: 0.304 AC: 4641 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1453 AN: 3466

East Asian (EAS) AF: 0.380 AC: 1961 AN: 5166

South Asian (SAS) AF: 0.315 AC: 1518 AN: 4816

European-Finnish (FIN) AF: 0.466 AC: 4920 AN: 10550

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.391 AC: 26579 AN: 67950

Other (OTH) AF: 0.416 AC: 878 AN: 2110

Alfa AF: 0.387 Hom.: 51379

Bravo AF: 0.376

Asia WGS AF: 0.386 AC: 1341 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.2
DANN	Benign	0.54
PhyloP100		-0.14

Splicing

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

Other links and lift over

dbSNP: rs1824936; hg19: chr5-153986044;