chr17-29348208-C-T

Position:

• chr17-29348208-C-T

Variant summary

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

The ENST00000685798.1(ENSG00000264808):​n.453-13679G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.433 in 151,608 control chromosomes in the GnomAD database, including 15,607 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 0.43 (15607 hom., cov: 30)
• Consequence: ENST00000685798.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.89

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.73).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.864 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000685798.1	n.453-13679G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.433 AC: 65617 AN: 151490 Hom.: 15581 Cov.: 30

Gnomad AFR AF: 0.576

Gnomad AMI AF: 0.419

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.322

Gnomad EAS AF: 0.885

Gnomad SAS AF: 0.507

Gnomad FIN AF: 0.380

Gnomad MID AF: 0.345

Gnomad NFE AF: 0.338

Gnomad OTH AF: 0.384

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

GnomAD4 genome AF: 0.433 AC: 65678 AN: 151608 Hom.: 15607 Cov.: 30 AF XY: 0.441 AC XY: 32691 AN XY: 74090

Gnomad4 AFR AF: 0.576

Gnomad4 AMR AF: 0.365

Gnomad4 ASJ AF: 0.322

Gnomad4 EAS AF: 0.885

Gnomad4 SAS AF: 0.504

Gnomad4 FIN AF: 0.380

Gnomad4 NFE AF: 0.338

Gnomad4 OTH AF: 0.386

Alfa AF: 0.358 Hom.: 15395

Bravo AF: 0.440

Asia WGS AF: 0.652 AC: 2271 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.73
CADD	Benign	8.1
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11653144; hg19: chr17-27675226;