chr5-160546827-T-C

Variant names:

• chr5-160546827-T-C
• rs12514981

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 0.0531 in 152,234 control chromosomes in the GnomAD database, including 287 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 0.053 (287 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.434

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0798 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: 0.0531 AC: 8079 AN: 152116 Hom.: 287 Cov.: 32

Gnomad AFR AF: 0.0147

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.0709

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0249

Gnomad FIN AF: 0.0457

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0816

Gnomad OTH AF: 0.0637

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

GnomAD4 genome AF: 0.0531 AC: 8077 AN: 152234 Hom.: 287 Cov.: 32 AF XY: 0.0510 AC XY: 3795 AN XY: 74428

Gnomad4 AFR AF: 0.0147

Gnomad4 AMR AF: 0.0540

Gnomad4 ASJ AF: 0.0709

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0249

Gnomad4 FIN AF: 0.0457

Gnomad4 NFE AF: 0.0816

Gnomad4 OTH AF: 0.0630

Alfa AF: 0.0744 Hom.: 278

Bravo AF: 0.0528

Asia WGS AF: 0.0130 AC: 49 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.46
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12514981; hg19: chr5-159973834;