rs891992

Variant names:

• chr5-147845951-T-C
• rs891992

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 0.179 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
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• 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

African (AFR) AF: 0.232 AC: 9619 AN: 41496

American (AMR) AF: 0.200 AC: 3053 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 745 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1591 AN: 5162

South Asian (SAS) AF: 0.160 AC: 774 AN: 4828

European-Finnish (FIN) AF: 0.121 AC: 1288 AN: 10614

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9613 AN: 67976

Other (OTH) AF: 0.181 AC: 384 AN: 2116

Alfa AF: 0.163 Hom.: 7997

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
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs891992; hg19: chr5-147225514;