5-165337081-A-G

Position:

• chr5-165337081-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 0.0956 in 152,254 control chromosomes in the GnomAD database, including 929 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 0.096 (929 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.366

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.139 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: 0.0957 AC: 14557 AN: 152136 Hom.: 930 Cov.: 32

Gnomad AFR AF: 0.0257

Gnomad AMI AF: 0.132

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.0524

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.124

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.0738

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

GnomAD4 genome AF: 0.0956 AC: 14550 AN: 152254 Hom.: 929 Cov.: 32 AF XY: 0.0934 AC XY: 6954 AN XY: 74436

Gnomad4 AFR AF: 0.0256

Gnomad4 AMR AF: 0.103

Gnomad4 ASJ AF: 0.0524

Gnomad4 EAS AF: 0.000387

Gnomad4 SAS AF: 0.107

Gnomad4 FIN AF: 0.124

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.0725

Alfa AF: 0.115 Hom.: 739

Bravo AF: 0.0905

Asia WGS AF: 0.0400 AC: 141 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.6
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1145652; hg19: chr5-164764087;