17-29387569-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 20 publications found

Genes affected

ENSG00000264808 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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

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

African (AFR) AF: 0.858 AC: 35177 AN: 41018

American (AMR) AF: 0.596 AC: 9032 AN: 15150

Ashkenazi Jewish (ASJ) AF: 0.549 AC: 1904 AN: 3470

East Asian (EAS) AF: 0.968 AC: 4941 AN: 5102

South Asian (SAS) AF: 0.642 AC: 3073 AN: 4790

European-Finnish (FIN) AF: 0.552 AC: 5681 AN: 10296

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.523 AC: 35446 AN: 67808

Other (OTH) AF: 0.592 AC: 1234 AN: 2086

Alfa AF: 0.562 Hom.: 33540

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
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs8076739; hg19: chr17-27714587;