5-161728308-C-G

Position:

• chr5-161728308-C-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 0.632 in 151,892 control chromosomes in the GnomAD database, including 30,522 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 0.63 (30522 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.00

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 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: 0.632 AC: 95917 AN: 151774 Hom.: 30474 Cov.: 32

Gnomad AFR AF: 0.616

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.699

Gnomad ASJ AF: 0.551

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.698

Gnomad FIN AF: 0.641

Gnomad MID AF: 0.601

Gnomad NFE AF: 0.614

Gnomad OTH AF: 0.639

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

GnomAD4 genome AF: 0.632 AC: 96019 AN: 151892 Hom.: 30522 Cov.: 32 AF XY: 0.637 AC XY: 47267 AN XY: 74222

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.699

Gnomad4 ASJ AF: 0.551

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.698

Gnomad4 FIN AF: 0.641

Gnomad4 NFE AF: 0.614

Gnomad4 OTH AF: 0.644

Alfa AF: 0.499 Hom.: 1356

Bravo AF: 0.636

Asia WGS AF: 0.750 AC: 2601 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.0080
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4128400; hg19: chr5-161155314;