5-161197451-C-T

Variant names:

• chr5-161197451-C-T
• rs164368

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.323 AC: 13388 AN: 41402

American (AMR) AF: 0.626 AC: 9551 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.630 AC: 2186 AN: 3470

East Asian (EAS) AF: 0.782 AC: 4020 AN: 5138

South Asian (SAS) AF: 0.623 AC: 2993 AN: 4808

European-Finnish (FIN) AF: 0.661 AC: 6977 AN: 10548

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.682 AC: 46311 AN: 67944

Other (OTH) AF: 0.606 AC: 1278 AN: 2108

Alfa AF: 0.647 Hom.: 102641

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
PhyloP100		-0.075

Splicing

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

Other links and lift over

dbSNP: rs164368; hg19: chr5-160624458;