chr5-153488877-T-C

Variant names:

• chr5-153488877-T-C
• rs548294

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 0.621 in 152,028 control chromosomes in the GnomAD database, including 29,601 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 0.62 (29601 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.481
• Publications: 17 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.702 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: 0.621 AC: 94407 AN: 151908 Hom.: 29585 Cov.: 32

Gnomad AFR AF: 0.641

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.678

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.722

Gnomad SAS AF: 0.687

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.644

Gnomad NFE AF: 0.606

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.621 AC: 94472 AN: 152028 Hom.: 29601 Cov.: 32 AF XY: 0.620 AC XY: 46040 AN XY: 74318

African (AFR) AF: 0.640 AC: 26568 AN: 41484

American (AMR) AF: 0.678 AC: 10364 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.569 AC: 1971 AN: 3466

East Asian (EAS) AF: 0.721 AC: 3720 AN: 5158

South Asian (SAS) AF: 0.686 AC: 3302 AN: 4812

European-Finnish (FIN) AF: 0.514 AC: 5429 AN: 10560

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.606 AC: 41165 AN: 67960

Other (OTH) AF: 0.607 AC: 1282 AN: 2112

Alfa AF: 0.616 Hom.: 61640

Bravo AF: 0.636

Asia WGS AF: 0.727 AC: 2527 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.4
DANN	Benign	0.48
PhyloP100		0.48

Splicing

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

Other links and lift over

dbSNP: rs548294; hg19: chr5-152868437;