chr5-118824240-A-C

Position:

• chr5-118824240-A-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 0.0435 in 152,116 control chromosomes in the GnomAD database, including 163 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 0.043 (163 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.931

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0649 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0434 AC: 6604 AN: 151998 Hom.: 162 Cov.: 32

Gnomad AFR AF: 0.0669

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.0493

Gnomad ASJ AF: 0.0101

Gnomad EAS AF: 0.0290

Gnomad SAS AF: 0.0186

Gnomad FIN AF: 0.0756

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0266

Gnomad OTH AF: 0.0445

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

GnomAD4 genome AF: 0.0435 AC: 6616 AN: 152116 Hom.: 163 Cov.: 32 AF XY: 0.0454 AC XY: 3377 AN XY: 74344

Gnomad4 AFR AF: 0.0670

Gnomad4 AMR AF: 0.0492

Gnomad4 ASJ AF: 0.0101

Gnomad4 EAS AF: 0.0290

Gnomad4 SAS AF: 0.0187

Gnomad4 FIN AF: 0.0756

Gnomad4 NFE AF: 0.0266

Gnomad4 OTH AF: 0.0445

Alfa AF: 0.0293 Hom.: 92

Bravo AF: 0.0441

Asia WGS AF: 0.0250 AC: 85 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.6
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17144687; hg19: chr5-118159935;