5-115034026-T-G

Position:

• chr5-115034026-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The variant allele was found at a frequency of 0.0318 in 152,296 control chromosomes in the GnomAD database, including 111 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 0.032 (111 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.345

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population eas. gnomad4 allele frequency = 0.0318 (4836/152296) while in subpopulation EAS AF= 0.0469 (243/5178). AF 95% confidence interval is 0.0421. There are 111 homozygotes in gnomad4. There are 2481 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 111 gene

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: 0.0317 AC: 4830 AN: 152178 Hom.: 112 Cov.: 33

Gnomad AFR AF: 0.00752

Gnomad AMI AF: 0.0373

Gnomad AMR AF: 0.0381

Gnomad ASJ AF: 0.0363

Gnomad EAS AF: 0.0466

Gnomad SAS AF: 0.0296

Gnomad FIN AF: 0.0784

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0364

Gnomad OTH AF: 0.0372

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

GnomAD4 genome AF: 0.0318 AC: 4836 AN: 152296 Hom.: 111 Cov.: 33 AF XY: 0.0333 AC XY: 2481 AN XY: 74468

Gnomad4 AFR AF: 0.00750

Gnomad4 AMR AF: 0.0384

Gnomad4 ASJ AF: 0.0363

Gnomad4 EAS AF: 0.0469

Gnomad4 SAS AF: 0.0298

Gnomad4 FIN AF: 0.0784

Gnomad4 NFE AF: 0.0364

Gnomad4 OTH AF: 0.0364

Alfa AF: 0.0362 Hom.: 120

Bravo AF: 0.0287

Asia WGS AF: 0.0540 AC: 186 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	0.71
DANN	Benign	0.58

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13176432; hg19: chr5-114369723;