5-115960385-T-G

Position:

• chr5-115960385-T-G

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 0.343 in 152,066 control chromosomes in the GnomAD database, including 9,265 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 0.34 (9265 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.277

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.389 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: 0.343 AC: 52184 AN: 151948 Hom.: 9259 Cov.: 32

Gnomad AFR AF: 0.308

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.282

Gnomad ASJ AF: 0.364

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.185

Gnomad FIN AF: 0.383

Gnomad MID AF: 0.373

Gnomad NFE AF: 0.393

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.343 AC: 52208 AN: 152066 Hom.: 9265 Cov.: 32 AF XY: 0.339 AC XY: 25167 AN XY: 74338

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.282

Gnomad4 ASJ AF: 0.364

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.185

Gnomad4 FIN AF: 0.383

Gnomad4 NFE AF: 0.393

Gnomad4 OTH AF: 0.339

Alfa AF: 0.359 Hom.: 1714

Bravo AF: 0.334

Asia WGS AF: 0.215 AC: 748 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	8.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6883910; hg19: chr5-115296082; COSMIC: COSV63496699;