rs17156916

chr5-104707159-T-C

Variant summary

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

The ENST00000503650.1(ENSG00000251574):n.328+179699A>G 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 0.139 in 152,074 control chromosomes in the GnomAD database, including 1,525 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 0.14 (1525 hom., cov: 32)
• Consequence: ENST00000503650.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.578

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379109	XR_948647.2	n.323+56121A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000503650.1	n.328+179699A>G		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.140 AC: 21205 AN: 151956 Hom.: 1527 Cov.: 32

Gnomad AFR AF: 0.114

Gnomad AMI AF: 0.107

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.139

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.185

Gnomad MID AF: 0.131

Gnomad NFE AF: 0.146

Gnomad OTH AF: 0.116

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

GnomAD4 genome AF: 0.139 AC: 21204 AN: 152074 Hom.: 1525 Cov.: 32 AF XY: 0.142 AC XY: 10536 AN XY: 74326

Gnomad4 AFR AF: 0.113

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.139

Gnomad4 EAS AF: 0.189

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.185

Gnomad4 NFE AF: 0.146

Gnomad4 OTH AF: 0.117

Alfa AF: 0.145 Hom.: 759

Bravo AF: 0.136

Asia WGS AF: 0.189 AC: 657 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.28
Dann	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17156916; hg19: chr5-104042860;