chr5-161197451-C-T

Variant names:

• chr5-161197451-C-T
• rs164368

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 0.577 in 151,874 control chromosomes in the GnomAD database, including 27,274 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 0.58 (27274 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0750

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.577 AC: 87556 AN: 151758 Hom.: 27259 Cov.: 30

Gnomad AFR AF: 0.324

Gnomad AMI AF: 0.780

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.630

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.661

Gnomad MID AF: 0.598

Gnomad NFE AF: 0.682

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.577 AC: 87596 AN: 151874 Hom.: 27274 Cov.: 30 AF XY: 0.579 AC XY: 42961 AN XY: 74220

Gnomad4 AFR AF: 0.323

Gnomad4 AMR AF: 0.626

Gnomad4 ASJ AF: 0.630

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.623

Gnomad4 FIN AF: 0.661

Gnomad4 NFE AF: 0.682

Gnomad4 OTH AF: 0.606

Alfa AF: 0.669 Hom.: 70009

Bravo AF: 0.564

Asia WGS AF: 0.688 AC: 2395 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.1
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs164368; hg19: chr5-160624458;