rs2142824

Variant names:

• chr22-36537621-G-A
• rs2142824

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 0.376 in 732,054 control chromosomes in the GnomAD database, including 52,632 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 0.39 (11927 hom., cov: 31)
  • Exomes 𝑓: 0.37 (40705 hom.)
• Consequence: LOC100500719 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0980
• Publications: 1 publications found

Genes affected

LOC100500719 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100500719		n.36537621G>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000188078	ENST00000339367.4	n.-17C>T		upstream_gene_variant		6

Frequencies

GnomAD3 genomes AF: 0.393 AC: 59659 AN: 151948 Hom.: 11902 Cov.: 31

Gnomad AFR AF: 0.449

Gnomad AMI AF: 0.444

Gnomad AMR AF: 0.383

Gnomad ASJ AF: 0.400

Gnomad EAS AF: 0.227

Gnomad SAS AF: 0.372

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.368

GnomAD4 exome AF: 0.372 AC: 215568 AN: 579988 Hom.: 40705 Cov.: 3 AF XY: 0.372 AC XY: 117626 AN XY: 315824

African (AFR) AF: 0.451 AC: 7495 AN: 16628

American (AMR) AF: 0.365 AC: 13760 AN: 37694

Ashkenazi Jewish (ASJ) AF: 0.402 AC: 7935 AN: 19760

East Asian (EAS) AF: 0.226 AC: 7699 AN: 34094

South Asian (SAS) AF: 0.391 AC: 25782 AN: 65886

European-Finnish (FIN) AF: 0.373 AC: 15721 AN: 42106

Middle Eastern (MID) AF: 0.440 AC: 1714 AN: 3892

European-Non Finnish (NFE) AF: 0.376 AC: 123729 AN: 328746

Other (OTH) AF: 0.376 AC: 11733 AN: 31182

GnomAD4 genome AF: 0.393 AC: 59723 AN: 152066 Hom.: 11927 Cov.: 31 AF XY: 0.390 AC XY: 28999 AN XY: 74326

African (AFR) AF: 0.449 AC: 18643 AN: 41476

American (AMR) AF: 0.383 AC: 5845 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.400 AC: 1387 AN: 3470

East Asian (EAS) AF: 0.227 AC: 1171 AN: 5156

South Asian (SAS) AF: 0.373 AC: 1795 AN: 4812

European-Finnish (FIN) AF: 0.382 AC: 4047 AN: 10584

Middle Eastern (MID) AF: 0.446 AC: 131 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25532 AN: 67980

Other (OTH) AF: 0.364 AC: 768 AN: 2108

Alfa AF: 0.387 Hom.: 2309

Bravo AF: 0.394

Asia WGS AF: 0.300 AC: 1041 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	0.18
DANN	Benign	0.57
PhyloP100		-0.098

Splicing

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

Other links and lift over

dbSNP: rs2142824; hg19: chr22-36933668; COSMIC: COSV59546486;