rs17760296

chr17-56538256-T-G

Variant summary

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

The XR_002958121.1(LOC112268194):n.245-422A>C 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 0.121 in 152,296 control chromosomes in the GnomAD database, including 1,455 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 0.12 (1455 hom., cov: 33)
• Consequence: LOC112268194 XR_002958121.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0640

Genes affected

LOC112268194 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC112268194	XR_002958121.1	n.245-422A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18366 AN: 152178 Hom.: 1457 Cov.: 33

Gnomad AFR AF: 0.0480

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.0845

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.0163

Gnomad SAS AF: 0.0613

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.141

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

GnomAD4 genome AF: 0.121 AC: 18356 AN: 152296 Hom.: 1455 Cov.: 33 AF XY: 0.123 AC XY: 9144 AN XY: 74476

Gnomad4 AFR AF: 0.0479

Gnomad4 AMR AF: 0.0845

Gnomad4 ASJ AF: 0.122

Gnomad4 EAS AF: 0.0164

Gnomad4 SAS AF: 0.0613

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.139

Alfa AF: 0.144 Hom.: 3859

Bravo AF: 0.103

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
Cadd	Benign	3.9
Dann	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs17760296; hg19: chr17-54615617;