chr17-6258704-C-G

Variant names:

• chr17-6258704-C-G
• rs12452660
• ENST00000761288.1:n.239-8024C>G

Variant summary

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

The ENST00000761288.1(ENSG00000299154):​n.239-8024C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,996 control chromosomes in the GnomAD database, including 7,007 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 0.29 (7007 hom., cov: 32)
• Consequence: ENSG00000299154 ENST00000761288.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.882
• Publications: 5 publications found

Genes affected

ENSG00000299154 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.388 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000299154	ENST00000761288.1	n.239-8024C>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44020 AN: 151876 Hom.: 6987 Cov.: 32

Gnomad AFR AF: 0.393

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.363

Gnomad ASJ AF: 0.218

Gnomad EAS AF: 0.270

Gnomad SAS AF: 0.313

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.264

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.277

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

GnomAD4 genome AF: 0.290 AC: 44084 AN: 151996 Hom.: 7007 Cov.: 32 AF XY: 0.293 AC XY: 21794 AN XY: 74304

African (AFR) AF: 0.393 AC: 16296 AN: 41438

American (AMR) AF: 0.364 AC: 5565 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.218 AC: 758 AN: 3470

East Asian (EAS) AF: 0.269 AC: 1388 AN: 5152

South Asian (SAS) AF: 0.313 AC: 1507 AN: 4818

European-Finnish (FIN) AF: 0.245 AC: 2578 AN: 10542

Middle Eastern (MID) AF: 0.271 AC: 79 AN: 292

European-Non Finnish (NFE) AF: 0.223 AC: 15162 AN: 67982

Other (OTH) AF: 0.273 AC: 577 AN: 2110

Alfa AF: 0.263 Hom.: 738

Bravo AF: 0.306

Asia WGS AF: 0.246 AC: 855 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.9
DANN	Benign	0.62
PhyloP100		0.88

Splicing

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

Other links and lift over

dbSNP: rs12452660; hg19: chr17-6162024;