17-29376331-C-T

Position:

• chr17-29376331-C-T

Variant summary

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

The variant allele was found at a frequency of 0.644 in 151,962 control chromosomes in the GnomAD database, including 33,388 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 (33388 hom., cov: 31)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.216

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• 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/exons	MANE	Protein	UniProt
		n.29376331C>T		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000264808	ENST00000577218.1	n.174-6026G>A		intron_variant		3
ENSG00000266111	ENST00000584958.2	n.39+24224C>T		intron_variant		5
ENSG00000264808	ENST00000685798.1	n.294-6026G>A		intron_variant
ENSG00000264808	ENST00000693027.1	n.295-6026G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.644 AC: 97763 AN: 151842 Hom.: 33336 Cov.: 31

Gnomad AFR AF: 0.858

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.552

Gnomad EAS AF: 0.968

Gnomad SAS AF: 0.645

Gnomad FIN AF: 0.552

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.523

Gnomad OTH AF: 0.585

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

GnomAD4 genome AF: 0.644 AC: 97867 AN: 151962 Hom.: 33388 Cov.: 31 AF XY: 0.647 AC XY: 48055 AN XY: 74264

Gnomad4 AFR AF: 0.858

Gnomad4 AMR AF: 0.596

Gnomad4 ASJ AF: 0.552

Gnomad4 EAS AF: 0.969

Gnomad4 SAS AF: 0.642

Gnomad4 FIN AF: 0.552

Gnomad4 NFE AF: 0.523

Gnomad4 OTH AF: 0.590

Alfa AF: 0.557 Hom.: 31677

Bravo AF: 0.656

Asia WGS AF: 0.827 AC: 2876 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.82
DANN	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2138852; hg19: chr17-27703349;