rs1186922

Variant names:

• chr5-157894180-T-A
• rs1186922

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 0.363 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
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -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

African (AFR) AF: 0.377 AC: 15633 AN: 41480

American (AMR) AF: 0.281 AC: 4293 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1266 AN: 3468

East Asian (EAS) AF: 0.266 AC: 1376 AN: 5182

South Asian (SAS) AF: 0.366 AC: 1764 AN: 4816

European-Finnish (FIN) AF: 0.422 AC: 4457 AN: 10568

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.375 AC: 25484 AN: 67984

Other (OTH) AF: 0.356 AC: 751 AN: 2112

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
PhyloP100		0.46

Splicing

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

Other links and lift over

dbSNP: rs1186922; hg19: chr5-157321188;