17-78352749-G-C

Variant names:

• chr17-78352749-G-C
• rs12944581
• XR_007065920.1:n.34C>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

Genes affected

LOC124904064 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000794841.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000303469	ENST00000794841.1		n.138+2374C>G		intron	N/A
	ENSG00000303469	ENST00000794842.1		n.135+654C>G		intron	N/A
	ENSG00000303469	ENST00000794843.1		n.101-202C>G		intron	N/A

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

African (AFR) AF: 0.615 AC: 25517 AN: 41464

American (AMR) AF: 0.717 AC: 10960 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.767 AC: 2662 AN: 3472

East Asian (EAS) AF: 0.743 AC: 3827 AN: 5148

South Asian (SAS) AF: 0.729 AC: 3518 AN: 4826

European-Finnish (FIN) AF: 0.688 AC: 7271 AN: 10574

Middle Eastern (MID) AF: 0.836 AC: 244 AN: 292

European-Non Finnish (NFE) AF: 0.724 AC: 49187 AN: 67948

Other (OTH) AF: 0.708 AC: 1498 AN: 2116

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	8.3
DANN	Benign	0.76
PhyloP100		-0.51

Splicing

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

Other links and lift over

dbSNP: rs12944581; hg19: chr17-76348830;