17-34246488-T-G

Variant names:

• chr17-34246488-T-G
• rs7210316
• ENST00000776537.1:n.238+5385A>C

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+5385A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 151,884 control chromosomes in the GnomAD database, including 8,828 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 (8828 hom., cov: 32)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.611
• Publications: 8 publications found

Genes affected

ENSG00000301139 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.539 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776537.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301139	ENST00000776537.1		n.238+5385A>C		intron	N/A
	ENSG00000301139	ENST00000776538.1		n.238+5385A>C		intron	N/A
	ENSG00000301139	ENST00000776539.1		n.236+5385A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50360 AN: 151766 Hom.: 8806 Cov.: 32

Gnomad AFR AF: 0.352

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.453

Gnomad ASJ AF: 0.316

Gnomad EAS AF: 0.555

Gnomad SAS AF: 0.357

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.275

Gnomad OTH AF: 0.322

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

GnomAD4 genome AF: 0.332 AC: 50428 AN: 151884 Hom.: 8828 Cov.: 32 AF XY: 0.340 AC XY: 25198 AN XY: 74210

African (AFR) AF: 0.352 AC: 14581 AN: 41366

American (AMR) AF: 0.454 AC: 6937 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.316 AC: 1095 AN: 3464

East Asian (EAS) AF: 0.556 AC: 2860 AN: 5146

South Asian (SAS) AF: 0.358 AC: 1725 AN: 4816

European-Finnish (FIN) AF: 0.343 AC: 3619 AN: 10540

Middle Eastern (MID) AF: 0.310 AC: 91 AN: 294

European-Non Finnish (NFE) AF: 0.275 AC: 18715 AN: 67960

Other (OTH) AF: 0.321 AC: 677 AN: 2106

Alfa AF: 0.303 Hom.: 1694

Bravo AF: 0.342

Asia WGS AF: 0.460 AC: 1599 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	0.14
DANN	Benign	0.40
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs7210316; hg19: chr17-32573507;