rs17075980

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377732	XR_001743001.1	n.524-4144C>T		intron_variant	Intron 3 of 14
LOC105377732	XR_007059057.1	n.1488+1386C>T		intron_variant	Intron 5 of 17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253141	ENST00000519400.2	n.261+1581C>T		intron_variant	Intron 1 of 2	3
ENSG00000253141	ENST00000662094.1	n.432+1386C>T		intron_variant	Intron 1 of 1
ENSG00000253968	ENST00000827042.1	n.271+13775C>T		intron_variant	Intron 1 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs17075980; hg19: chr5-172892328;