5-132667152-C-T

Variant names:

• chr5-132667152-C-T
• rs2243221

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 0.17 in 152,162 control chromosomes in the GnomAD database, including 3,662 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 0.17 (3662 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.381 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: 0.170 AC: 25854 AN: 152044 Hom.: 3646 Cov.: 32

Gnomad AFR AF: 0.385

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.141

Gnomad EAS AF: 0.0390

Gnomad SAS AF: 0.143

Gnomad FIN AF: 0.0438

Gnomad MID AF: 0.190

Gnomad NFE AF: 0.0802

Gnomad OTH AF: 0.156

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

GnomAD4 genome AF: 0.170 AC: 25913 AN: 152162 Hom.: 3662 Cov.: 32 AF XY: 0.167 AC XY: 12450 AN XY: 74406

African (AFR) AF: 0.386 AC: 16001 AN: 41472

American (AMR) AF: 0.142 AC: 2166 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.141 AC: 489 AN: 3468

East Asian (EAS) AF: 0.0393 AC: 204 AN: 5194

South Asian (SAS) AF: 0.143 AC: 689 AN: 4820

European-Finnish (FIN) AF: 0.0438 AC: 465 AN: 10610

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.0803 AC: 5459 AN: 67996

Other (OTH) AF: 0.154 AC: 325 AN: 2112

Alfa AF: 0.0940 Hom.: 238

Bravo AF: 0.188

Asia WGS AF: 0.118 AC: 410 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.3
DANN	Benign	0.54
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs2243221; hg19: chr5-132002844;