5-173465325-C-T

Variant names:

• chr5-173465325-C-T
• rs17075980
• ENST00000519400.2:n.261+1581C>T

Variant summary

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

The ENST00000519400.2(ENSG00000253141):​n.261+1581C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.297 in 152,126 control chromosomes in the GnomAD database, including 8,703 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 0.30 (8703 hom., cov: 33)
• Consequence: ENSG00000253141 ENST00000519400.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 3 publications found

Genes affected

ENSG00000253141 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000519400.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000253141	ENST00000519400.2	TSL:3	n.261+1581C>T		intron	N/A
	ENSG00000253141	ENST00000662094.1		n.432+1386C>T		intron	N/A
	ENSG00000253968	ENST00000827042.1		n.271+13775C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.296 AC: 45068 AN: 152006 Hom.: 8674 Cov.: 33

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.145

Gnomad AMR AF: 0.188

Gnomad ASJ AF: 0.223

Gnomad EAS AF: 0.0940

Gnomad SAS AF: 0.103

Gnomad FIN AF: 0.268

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.297 AC: 45146 AN: 152126 Hom.: 8703 Cov.: 33 AF XY: 0.291 AC XY: 21658 AN XY: 74372

African (AFR) AF: 0.550 AC: 22796 AN: 41462

American (AMR) AF: 0.188 AC: 2882 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.223 AC: 771 AN: 3464

East Asian (EAS) AF: 0.0942 AC: 489 AN: 5190

South Asian (SAS) AF: 0.102 AC: 495 AN: 4830

European-Finnish (FIN) AF: 0.268 AC: 2831 AN: 10580

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14177 AN: 67994

Other (OTH) AF: 0.250 AC: 527 AN: 2104

Alfa AF: 0.226 Hom.: 8616

Bravo AF: 0.305

Asia WGS AF: 0.116 AC: 406 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.026
DANN	Benign	0.26
PhyloP100		-1.6

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs17075980;

hg19: chr5-172892328;