17-34223845-T-C

Variant names:

• chr17-34223845-T-C
• rs1029719
• ENST00000776537.1:n.239-4424A>G

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.239-4424A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.651 in 151,936 control chromosomes in the GnomAD database, including 32,620 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 0.65 (32620 hom., cov: 31)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0580
• Publications: 6 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=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.838 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
ENSG00000301139	ENST00000776537.1	n.239-4424A>G		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776538.1	n.239-706A>G		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776539.1	n.237-753A>G		intron_variant	Intron 2 of 2
ENSG00000301139	ENST00000776540.1	n.159-753A>G		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.651 AC: 98793 AN: 151818 Hom.: 32574 Cov.: 31

Gnomad AFR AF: 0.688

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.730

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.630

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.590

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.651 AC: 98900 AN: 151936 Hom.: 32620 Cov.: 31 AF XY: 0.660 AC XY: 49039 AN XY: 74254

African (AFR) AF: 0.689 AC: 28533 AN: 41428

American (AMR) AF: 0.730 AC: 11158 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3468

East Asian (EAS) AF: 0.859 AC: 4424 AN: 5152

South Asian (SAS) AF: 0.817 AC: 3935 AN: 4816

European-Finnish (FIN) AF: 0.630 AC: 6643 AN: 10538

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.590 AC: 40064 AN: 67942

Other (OTH) AF: 0.651 AC: 1374 AN: 2112

Alfa AF: 0.615 Hom.: 36449

Bravo AF: 0.657

Asia WGS AF: 0.835 AC: 2902 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.71
PhyloP100		-0.058

Splicing

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

Other links and lift over

dbSNP: rs1029719; hg19: chr17-32550864;