chr17-35982014-C-A

Variant names:

• chr17-35982014-C-A
• rs854680
• ENST00000789008.1:n.807C>A

Variant summary

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

The ENST00000789008.1(ENSG00000302706):​n.807C>A 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 0.329 in 150,308 control chromosomes in the GnomAD database, including 10,288 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 0.33 (10288 hom., cov: 28)
• Consequence: ENSG00000302706 ENST00000789008.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 23 publications found

Genes affected

ENSG00000302706 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (Cadd=0.265).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.582 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
ENSG00000302706	ENST00000789008.1	n.807C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000302706	ENST00000789009.1	n.939C>A		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000270240	ENST00000788510.1	n.149-15185C>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.329 AC: 49408 AN: 150196 Hom.: 10274 Cov.: 28

Gnomad AFR AF: 0.588

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.301

Gnomad ASJ AF: 0.220

Gnomad EAS AF: 0.408

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.208

Gnomad OTH AF: 0.309

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

GnomAD4 genome AF: 0.329 AC: 49459 AN: 150308 Hom.: 10288 Cov.: 28 AF XY: 0.328 AC XY: 23999 AN XY: 73238

African (AFR) AF: 0.588 AC: 23891 AN: 40614

American (AMR) AF: 0.301 AC: 4551 AN: 15140

Ashkenazi Jewish (ASJ) AF: 0.220 AC: 762 AN: 3466

East Asian (EAS) AF: 0.406 AC: 2071 AN: 5096

South Asian (SAS) AF: 0.364 AC: 1710 AN: 4704

European-Finnish (FIN) AF: 0.132 AC: 1345 AN: 10208

Middle Eastern (MID) AF: 0.303 AC: 88 AN: 290

European-Non Finnish (NFE) AF: 0.208 AC: 14111 AN: 67792

Other (OTH) AF: 0.307 AC: 642 AN: 2088

Alfa AF: 0.254 Hom.: 11529

Bravo AF: 0.354

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
CADD	Benign	0.27
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs854680; hg19: -;