rs1469149

Variant names:

• chr5-132073149-A-C
• rs1469149

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 0.384 in 152,050 control chromosomes in the GnomAD database, including 12,103 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 0.38 (12103 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0910
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.489 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: 0.384 AC: 58387 AN: 151932 Hom.: 12089 Cov.: 33

Gnomad AFR AF: 0.495

Gnomad AMI AF: 0.593

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.310

Gnomad EAS AF: 0.00328

Gnomad SAS AF: 0.118

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.397

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.384 AC: 58427 AN: 152050 Hom.: 12103 Cov.: 33 AF XY: 0.369 AC XY: 27409 AN XY: 74348

African (AFR) AF: 0.495 AC: 20519 AN: 41476

American (AMR) AF: 0.329 AC: 5024 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.310 AC: 1075 AN: 3466

East Asian (EAS) AF: 0.00329 AC: 17 AN: 5172

South Asian (SAS) AF: 0.118 AC: 568 AN: 4828

European-Finnish (FIN) AF: 0.267 AC: 2825 AN: 10586

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.397 AC: 26990 AN: 67920

Other (OTH) AF: 0.380 AC: 801 AN: 2106

Alfa AF: 0.408 Hom.: 7785

Bravo AF: 0.398

Asia WGS AF: 0.0840 AC: 293 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.9
DANN	Benign	0.65
PhyloP100		-0.091

Splicing

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

Other links and lift over

dbSNP: rs1469149; hg19: chr5-131408842; COSMIC: COSV51522285;