rs891992

Variant names:

• chr5-147845951-T-C
• rs891992

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 0.179 in 152,140 control chromosomes in the GnomAD database, including 2,662 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 0.18 (2662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.718

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.296 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: 0.179 AC: 27264 AN: 152022 Hom.: 2656 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.199

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.309

Gnomad SAS AF: 0.161

Gnomad FIN AF: 0.121

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.181

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

GnomAD4 genome AF: 0.179 AC: 27309 AN: 152140 Hom.: 2662 Cov.: 32 AF XY: 0.177 AC XY: 13184 AN XY: 74386

Gnomad4 AFR AF: 0.232

Gnomad4 AMR AF: 0.200

Gnomad4 ASJ AF: 0.215

Gnomad4 EAS AF: 0.308

Gnomad4 SAS AF: 0.160

Gnomad4 FIN AF: 0.121

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.181

Alfa AF: 0.157 Hom.: 3143

Bravo AF: 0.193

Asia WGS AF: 0.224 AC: 780 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	3.9
DANN	Benign	0.80

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs891992; hg19: chr5-147225514;