chr17-34247262-A-T

Variant names:

• chr17-34247262-A-T
• rs8068314
• ENST00000776537.1:n.238+4611T>A

Variant summary

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

The ENST00000776537.1(ENSG00000301139):​n.238+4611T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.103 in 152,328 control chromosomes in the GnomAD database, including 984 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 0.10 (984 hom., cov: 33)
• Consequence: ENSG00000301139 ENST00000776537.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.951
• Publications: 5 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 (AFR) allele frequency at 95% confidence interval = 0.174 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+4611T>A		intron	N/A
	ENSG00000301139	ENST00000776538.1		n.238+4611T>A		intron	N/A
	ENSG00000301139	ENST00000776539.1		n.236+4611T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.103 AC: 15694 AN: 152210 Hom.: 980 Cov.: 33

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0811

Gnomad AMR AF: 0.0739

Gnomad ASJ AF: 0.0521

Gnomad EAS AF: 0.000960

Gnomad SAS AF: 0.0947

Gnomad FIN AF: 0.0662

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.0814

Gnomad OTH AF: 0.107

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

GnomAD4 genome AF: 0.103 AC: 15706 AN: 152328 Hom.: 984 Cov.: 33 AF XY: 0.101 AC XY: 7543 AN XY: 74500

African (AFR) AF: 0.177 AC: 7359 AN: 41552

American (AMR) AF: 0.0738 AC: 1130 AN: 15314

Ashkenazi Jewish (ASJ) AF: 0.0521 AC: 181 AN: 3472

East Asian (EAS) AF: 0.000962 AC: 5 AN: 5196

South Asian (SAS) AF: 0.0946 AC: 457 AN: 4832

European-Finnish (FIN) AF: 0.0662 AC: 703 AN: 10614

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0814 AC: 5535 AN: 68028

Other (OTH) AF: 0.105 AC: 223 AN: 2114

Alfa AF: 0.0924 Hom.: 95

Bravo AF: 0.106

Asia WGS AF: 0.0440 AC: 153 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	4.4
DANN	Benign	0.88
PhyloP100		0.95

Splicing

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

Other links and lift over

dbSNP: rs8068314; hg19: chr17-32574281;