17-78352749-G-C

Position:

• chr17-78352749-G-C

Variant summary

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

The XR_007065920.1(LOC124904064):​n.34C>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.694 in 152,040 control chromosomes in the GnomAD database, including 36,834 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 0.69 (36834 hom., cov: 32)
• Consequence: LOC124904064 XR_007065920.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.508

Genes affected

LOC124904064 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.724 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124904064	XR_007065920.1	n.34C>G		non_coding_transcript_exon_variant	1/2

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.694 AC: 105405 AN: 151922 Hom.: 36817 Cov.: 32

Gnomad AFR AF: 0.615

Gnomad AMI AF: 0.870

Gnomad AMR AF: 0.717

Gnomad ASJ AF: 0.767

Gnomad EAS AF: 0.743

Gnomad SAS AF: 0.731

Gnomad FIN AF: 0.688

Gnomad MID AF: 0.825

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.694 AC: 105474 AN: 152040 Hom.: 36834 Cov.: 32 AF XY: 0.694 AC XY: 51559 AN XY: 74326

Gnomad4 AFR AF: 0.615

Gnomad4 AMR AF: 0.717

Gnomad4 ASJ AF: 0.767

Gnomad4 EAS AF: 0.743

Gnomad4 SAS AF: 0.729

Gnomad4 FIN AF: 0.688

Gnomad4 NFE AF: 0.724

Gnomad4 OTH AF: 0.708

Alfa AF: 0.703 Hom.: 4442

Bravo AF: 0.692

Asia WGS AF: 0.724 AC: 2518 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.76

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs12944581; hg19: chr17-76348830;