5-173508176-T-A

Variant names:

• chr5-173508176-T-A
• rs11738751
• ENST00000827042.1:n.446+1804T>A

Variant summary

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

The ENST00000827042.1(ENSG00000253968):​n.446+1804T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,912 control chromosomes in the GnomAD database, including 10,385 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 0.37 (10385 hom., cov: 31)
• Consequence: ENSG00000253968 ENST00000827042.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 2 publications found

Genes affected

ENSG00000253968 (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 (AMR) allele frequency at 95% confidence interval = 0.453 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827042.1. 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
	ENSG00000253968	ENST00000827042.1		n.446+1804T>A		intron	N/A
	ENSG00000253968	ENST00000827044.1		n.374+1804T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.365 AC: 55468 AN: 151794 Hom.: 10362 Cov.: 31

Gnomad AFR AF: 0.293

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.329

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.402

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.320

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.387

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

GnomAD4 genome AF: 0.366 AC: 55538 AN: 151912 Hom.: 10385 Cov.: 31 AF XY: 0.369 AC XY: 27381 AN XY: 74248

African (AFR) AF: 0.293 AC: 12165 AN: 41448

American (AMR) AF: 0.462 AC: 7056 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.329 AC: 1139 AN: 3466

East Asian (EAS) AF: 0.272 AC: 1404 AN: 5170

South Asian (SAS) AF: 0.403 AC: 1944 AN: 4818

European-Finnish (FIN) AF: 0.388 AC: 4084 AN: 10514

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26434 AN: 67912

Other (OTH) AF: 0.392 AC: 827 AN: 2110

Alfa AF: 0.384 Hom.: 1401

Bravo AF: 0.368

Asia WGS AF: 0.346 AC: 1204 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.0
DANN	Benign	0.65
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs11738751; hg19: chr5-172935179; COSMIC: COSV60232134;