rs891992

Positions:

• chr5-147845951-T-C

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;