rs17411480

Variant names:

• chr6-30455340-C-G
• rs17411480
• ENST00000658719.1:n.2324C>G

Variant summary

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

The ENST00000658719.1(ENSG00000286301):​n.2324C>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 0.164 in 152,084 control chromosomes in the GnomAD database, including 2,231 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 0.16 (2231 hom., cov: 32)
• Consequence: ENSG00000286301 ENST00000658719.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.442
• Publications: 14 publications found

Genes affected

ENSG00000286301 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.237 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658719.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000286301	ENST00000658719.1		n.2324C>G		non_coding_transcript_exon	Exon 2 of 2

Frequencies

GnomAD3 genomes AF: 0.164 AC: 24892 AN: 151966 Hom.: 2231 Cov.: 32

Gnomad AFR AF: 0.242

Gnomad AMI AF: 0.147

Gnomad AMR AF: 0.107

Gnomad ASJ AF: 0.134

Gnomad EAS AF: 0.0310

Gnomad SAS AF: 0.141

Gnomad FIN AF: 0.0893

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.154

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

GnomAD4 genome AF: 0.164 AC: 24907 AN: 152084 Hom.: 2231 Cov.: 32 AF XY: 0.159 AC XY: 11824 AN XY: 74356

African (AFR) AF: 0.241 AC: 10003 AN: 41464

American (AMR) AF: 0.106 AC: 1626 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.134 AC: 465 AN: 3468

East Asian (EAS) AF: 0.0313 AC: 162 AN: 5184

South Asian (SAS) AF: 0.142 AC: 685 AN: 4816

European-Finnish (FIN) AF: 0.0893 AC: 945 AN: 10586

Middle Eastern (MID) AF: 0.0952 AC: 28 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10538 AN: 67980

Other (OTH) AF: 0.152 AC: 321 AN: 2112

Alfa AF: 0.158 Hom.: 308

Bravo AF: 0.171

Asia WGS AF: 0.0740 AC: 255 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.25
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs17411480; hg19: chr6-30423117;