ENST00000809623.1:n.178-7409T>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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000809623.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253673	ENST00000809623.1		n.178-7409T>G		intron	N/A
	ENSG00000253673	ENST00000809624.1		n.142-6135T>G		intron	N/A
	ENSG00000253673	ENST00000809626.1		n.104-7409T>G		intron	N/A

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 v4.9

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;