rs17658295

Positions:

• chr5-172774971-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000523005.1(ENSG00000253736):​n.70-2521G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,068 control chromosomes in the GnomAD database, including 8,408 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 0.32 (8408 hom., cov: 33)
• Consequence: ENST00000523005.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.312

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.38 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105377730	XR_941232.3	n.1129+2484G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000523005.1	n.70-2521G>A		intron_variant, non_coding_transcript_variant		3
	ENST00000687811.1	n.255+2484G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.321 AC: 48712 AN: 151952 Hom.: 8406 Cov.: 33

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.489

Gnomad AMR AF: 0.357

Gnomad ASJ AF: 0.339

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.295

Gnomad FIN AF: 0.392

Gnomad MID AF: 0.370

Gnomad NFE AF: 0.384

Gnomad OTH AF: 0.351

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

GnomAD4 genome AF: 0.320 AC: 48731 AN: 152068 Hom.: 8408 Cov.: 33 AF XY: 0.321 AC XY: 23849 AN XY: 74314

Gnomad4 AFR AF: 0.194

Gnomad4 AMR AF: 0.356

Gnomad4 ASJ AF: 0.339

Gnomad4 EAS AF: 0.216

Gnomad4 SAS AF: 0.296

Gnomad4 FIN AF: 0.392

Gnomad4 NFE AF: 0.384

Gnomad4 OTH AF: 0.346

Alfa AF: 0.377 Hom.: 10082

Bravo AF: 0.315

Asia WGS AF: 0.250 AC: 871 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	2.8
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17658295; hg19: chr5-172201974; COSMIC: COSV53319845;