chr5-10174546-A-G

Position:

• chr5-10174546-A-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 0.355 in 152,150 control chromosomes in the GnomAD database, including 10,465 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 0.36 (10465 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.807

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.438 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: 0.356 AC: 54055 AN: 152030 Hom.: 10463 Cov.: 32

Gnomad AFR AF: 0.208

Gnomad AMI AF: 0.495

Gnomad AMR AF: 0.447

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.136

Gnomad SAS AF: 0.351

Gnomad FIN AF: 0.401

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.363

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

GnomAD4 genome AF: 0.355 AC: 54081 AN: 152150 Hom.: 10465 Cov.: 32 AF XY: 0.352 AC XY: 26211 AN XY: 74374

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.447

Gnomad4 ASJ AF: 0.433

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.351

Gnomad4 FIN AF: 0.401

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.362

Alfa AF: 0.376 Hom.: 1429

Bravo AF: 0.356

Asia WGS AF: 0.230 AC: 804 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	6.3
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2386592; hg19: chr5-10174658;