NR_188292.1:n.185+260C>A

Variant names:

• chr17-67717234-G-T
• rs3760220
• ENST00000832642.1:n.493C>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_188292.1(LOC101928045):​n.185+260C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.898 in 152,232 control chromosomes in the GnomAD database, including 61,430 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 0.90 (61430 hom., cov: 33)
• Consequence: LOC101928045 NR_188292.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.286
• Publications: 2 publications found

Genes affected

ENSG00000288109 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.933 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NR_188292.1. 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
	LOC101928045	NR_188292.1		n.185+260C>A		intron	N/A
	LOC101928045	NR_188293.1		n.37+408C>A		intron	N/A
	LOC101928045	NR_188294.1		n.37+408C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288109	ENST00000832642.1		n.493C>A		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000288109	ENST00000832617.1		n.198-27861C>A		intron	N/A
	ENSG00000288109	ENST00000832618.1		n.212-27861C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.898 AC: 136551 AN: 152114 Hom.: 61375 Cov.: 33

Gnomad AFR AF: 0.925

Gnomad AMI AF: 0.787

Gnomad AMR AF: 0.904

Gnomad ASJ AF: 0.824

Gnomad EAS AF: 0.955

Gnomad SAS AF: 0.885

Gnomad FIN AF: 0.909

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.879

Gnomad OTH AF: 0.911

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

GnomAD4 genome AF: 0.898 AC: 136664 AN: 152232 Hom.: 61430 Cov.: 33 AF XY: 0.899 AC XY: 66909 AN XY: 74432

African (AFR) AF: 0.925 AC: 38401 AN: 41530

American (AMR) AF: 0.905 AC: 13829 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.824 AC: 2857 AN: 3466

East Asian (EAS) AF: 0.955 AC: 4954 AN: 5188

South Asian (SAS) AF: 0.885 AC: 4273 AN: 4828

European-Finnish (FIN) AF: 0.909 AC: 9646 AN: 10610

Middle Eastern (MID) AF: 0.901 AC: 265 AN: 294

European-Non Finnish (NFE) AF: 0.879 AC: 59801 AN: 68010

Other (OTH) AF: 0.912 AC: 1922 AN: 2108

Alfa AF: 0.886 Hom.: 94143

Bravo AF: 0.901

Asia WGS AF: 0.892 AC: 3101 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.1
DANN	Benign	0.61
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs3760220; hg19: chr17-65713350;