chr5-158198198-A-G

Variant names:

• chr5-158198198-A-G
• rs44156
• ENST00000522975.1:n.142-1279A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000522975.1(ENSG00000253673):​n.142-1279A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.312 in 152,080 control chromosomes in the GnomAD database, including 8,540 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 0.31 (8540 hom., cov: 32)
• Consequence: ENSG00000253673 ENST00000522975.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.269
• Publications: 3 publications found

Genes affected

ENSG00000253673 (HGNC:):

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 = 0.494 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
ENSG00000253673	ENST00000522975.1	n.142-1279A>G		intron_variant	Intron 1 of 1	3
ENSG00000253673	ENST00000809623.1	n.177+22662A>G		intron_variant	Intron 1 of 1
ENSG00000253673	ENST00000809624.1	n.39-7948A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.312 AC: 47402 AN: 151962 Hom.: 8507 Cov.: 32

Gnomad AFR AF: 0.499

Gnomad AMI AF: 0.233

Gnomad AMR AF: 0.213

Gnomad ASJ AF: 0.222

Gnomad EAS AF: 0.221

Gnomad SAS AF: 0.312

Gnomad FIN AF: 0.224

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.279

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

GnomAD4 genome AF: 0.312 AC: 47484 AN: 152080 Hom.: 8540 Cov.: 32 AF XY: 0.311 AC XY: 23098 AN XY: 74348

African (AFR) AF: 0.499 AC: 20691 AN: 41448

American (AMR) AF: 0.213 AC: 3249 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.222 AC: 769 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1143 AN: 5172

South Asian (SAS) AF: 0.312 AC: 1505 AN: 4818

European-Finnish (FIN) AF: 0.224 AC: 2371 AN: 10588

Middle Eastern (MID) AF: 0.381 AC: 112 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16832 AN: 67994

Other (OTH) AF: 0.284 AC: 600 AN: 2110

Alfa AF: 0.266 Hom.: 2269

Bravo AF: 0.313

Asia WGS AF: 0.350 AC: 1216 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	9.5
DANN	Benign	0.79
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs44156; hg19: chr5-157625206;