5-155434249-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.181 in 152,150 control chromosomes in the GnomAD database, including 2,850 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 0.18 (2850 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00300

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.28 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.181 AC: 27519 AN: 152032 Hom.: 2844 Cov.: 32

Gnomad AFR AF: 0.285

Gnomad AMI AF: 0.333

Gnomad AMR AF: 0.136

Gnomad ASJ AF: 0.152

Gnomad EAS AF: 0.0398

Gnomad SAS AF: 0.171

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.151

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.181 AC: 27543 AN: 152150 Hom.: 2850 Cov.: 32 AF XY: 0.177 AC XY: 13139 AN XY: 74384

Gnomad4 AFR AF: 0.284

Gnomad4 AMR AF: 0.135

Gnomad4 ASJ AF: 0.152

Gnomad4 EAS AF: 0.0398

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.105

Gnomad4 NFE AF: 0.151

Gnomad4 OTH AF: 0.179

Alfa AF: 0.133 Hom.: 728

Bravo AF: 0.187

Asia WGS AF: 0.120 AC: 418 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
Cadd	Benign	8.6
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10476823; hg19: chr5-154813809; COSMIC: COSV60217995;