rs1186922

Variant names:

• chr5-157894180-T-A
• rs1186922

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 0.363 in 152,096 control chromosomes in the GnomAD database, including 10,158 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 0.36 (10158 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.457

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.372 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: 0.363 AC: 55196 AN: 151978 Hom.: 10156 Cov.: 32

Gnomad AFR AF: 0.377

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.281

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.265

Gnomad SAS AF: 0.367

Gnomad FIN AF: 0.422

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.375

Gnomad OTH AF: 0.354

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

GnomAD4 genome AF: 0.363 AC: 55221 AN: 152096 Hom.: 10158 Cov.: 32 AF XY: 0.363 AC XY: 26979 AN XY: 74346

Gnomad4 AFR AF: 0.377

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.365

Gnomad4 EAS AF: 0.266

Gnomad4 SAS AF: 0.366

Gnomad4 FIN AF: 0.422

Gnomad4 NFE AF: 0.375

Gnomad4 OTH AF: 0.356

Alfa AF: 0.372 Hom.: 1493

Bravo AF: 0.348

Asia WGS AF: 0.285 AC: 994 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	13
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1186922; hg19: chr5-157321188;