chr17-29387569-C-T

Variant names:

• chr17-29387569-C-T
• rs8076739
• ENST00000577218.1:n.173+3036G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000577218.1(ENSG00000264808):​n.173+3036G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.643 in 150,910 control chromosomes in the GnomAD database, including 33,087 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 0.64 (33087 hom., cov: 27)
• Consequence: ENSG00000264808 ENST00000577218.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.919

Genes affected

ENSG00000264808 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.946 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
ENSG00000264808	ENST00000577218.1	n.173+3036G>A		intron_variant	Intron 1 of 1	3
ENSG00000266111	ENST00000584958.2	n.40-16157C>T		intron_variant	Intron 1 of 1	5
ENSG00000264808	ENST00000685798.1	n.293+2368G>A		intron_variant	Intron 1 of 2
ENSG00000264808	ENST00000693027.1	n.294+2368G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.643 AC: 97004 AN: 150794 Hom.: 33035 Cov.: 27

Gnomad AFR AF: 0.857

Gnomad AMI AF: 0.520

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.549

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.528

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.587

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

GnomAD4 genome AF: 0.643 AC: 97106 AN: 150910 Hom.: 33087 Cov.: 27 AF XY: 0.647 AC XY: 47613 AN XY: 73634

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.549

Gnomad4 EAS AF: 0.968

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.592

Alfa AF: 0.594 Hom.: 3716

Bravo AF: 0.656

Asia WGS AF: 0.826 AC: 2874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.79
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs8076739; hg19: chr17-27714587;