5-143438042-G-A

Variant names:

• chr5-143438042-G-A
• rs12521436

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 0.21 in 151,992 control chromosomes in the GnomAD database, including 3,706 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 0.21 (3706 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.397
• Publications: 16 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 (EAS) allele frequency at 95% confidence interval = 0.415 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: 0.210 AC: 31898 AN: 151874 Hom.: 3703 Cov.: 32

Gnomad AFR AF: 0.259

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.247

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.430

Gnomad SAS AF: 0.222

Gnomad FIN AF: 0.133

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.171

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.210 AC: 31937 AN: 151992 Hom.: 3706 Cov.: 32 AF XY: 0.209 AC XY: 15556 AN XY: 74326

African (AFR) AF: 0.259 AC: 10743 AN: 41446

American (AMR) AF: 0.247 AC: 3776 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 553 AN: 3470

East Asian (EAS) AF: 0.430 AC: 2212 AN: 5140

South Asian (SAS) AF: 0.221 AC: 1065 AN: 4810

European-Finnish (FIN) AF: 0.133 AC: 1401 AN: 10560

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.171 AC: 11612 AN: 67962

Other (OTH) AF: 0.208 AC: 438 AN: 2110

Alfa AF: 0.189 Hom.: 9181

Bravo AF: 0.223

Asia WGS AF: 0.279 AC: 972 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	2.6
DANN	Benign	0.29
PhyloP100		0.40

Splicing

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

Other links and lift over

dbSNP: rs12521436; hg19: chr5-142817607;