5-178999318-T-C

Position:

• chr5-178999318-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 0.624 in 150,550 control chromosomes in the GnomAD database, including 29,898 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 (29898 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.691 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: 0.624 AC: 93890 AN: 150442 Hom.: 29878 Cov.: 26

Gnomad AFR AF: 0.497

Gnomad AMI AF: 0.769

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.603

Gnomad FIN AF: 0.656

Gnomad MID AF: 0.691

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.619

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

GnomAD4 genome AF: 0.624 AC: 93947 AN: 150550 Hom.: 29898 Cov.: 26 AF XY: 0.622 AC XY: 45634 AN XY: 73364

Gnomad4 AFR AF: 0.497

Gnomad4 AMR AF: 0.648

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.604

Gnomad4 FIN AF: 0.656

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.617

Alfa AF: 0.553 Hom.: 2151

Bravo AF: 0.617

Asia WGS AF: 0.522 AC: 1817 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.24
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11249608; hg19: chr5-178426319; COSMIC: COSV51437372;