5-158243581-T-G

Variant names:

• chr5-158243581-T-G
• rs1173466
• ENST00000809623.1:n.178-7409T>G

Variant summary

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

The ENST00000809623.1(ENSG00000253673):​n.178-7409T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.48 in 151,916 control chromosomes in the GnomAD database, including 18,333 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 0.48 (18333 hom., cov: 31)
• Consequence: ENSG00000253673 ENST00000809623.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.16
• Publications: 1 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=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.621 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377678	XR_001742535.2	n.86+2113T>G		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253673	ENST00000809623.1	n.178-7409T>G		intron_variant	Intron 1 of 1
ENSG00000253673	ENST00000809624.1	n.142-6135T>G		intron_variant	Intron 2 of 3
ENSG00000253673	ENST00000809626.1	n.104-7409T>G		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.480 AC: 72864 AN: 151798 Hom.: 18290 Cov.: 31

Gnomad AFR AF: 0.627

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.373

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.389

Gnomad MID AF: 0.459

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.480 AC: 72962 AN: 151916 Hom.: 18333 Cov.: 31 AF XY: 0.477 AC XY: 35424 AN XY: 74242

African (AFR) AF: 0.628 AC: 25966 AN: 41372

American (AMR) AF: 0.456 AC: 6966 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.373 AC: 1294 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1320 AN: 5172

South Asian (SAS) AF: 0.376 AC: 1815 AN: 4822

European-Finnish (FIN) AF: 0.389 AC: 4111 AN: 10570

Middle Eastern (MID) AF: 0.442 AC: 130 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30091 AN: 67930

Other (OTH) AF: 0.453 AC: 956 AN: 2112

Alfa AF: 0.312 Hom.: 749

Bravo AF: 0.488

Asia WGS AF: 0.406 AC: 1413 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	9.7
DANN	Benign	0.59
PhyloP100		1.2

Splicing

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

Other links and lift over

dbSNP: rs1173466; hg19: chr5-157670589; COSMIC: COSV60220943;