6-63379079-A-T

Variant summary

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

The ENST00000701584.1(ENSG00000289911):n.672-6T>A variant causes a splice region, splice polypyrimidine tract, intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.162 in 152,164 control chromosomes in the GnomAD database, including 4,010 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 0.16 (4010 hom., cov: 32)
• Consequence: ENST00000701584.1 splice_region, splice_polypyrimidine_tract, intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.633

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LGSN	XM_011535892.4	c.-303+217T>A		intron_variant
LGSN	XM_017010930.3	c.-288+217T>A		intron_variant
LGSN	XM_047418866.1	c.-288+217T>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000701584.1	n.672-6T>A		splice_region_variant, splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24569 AN: 152046 Hom.: 3982 Cov.: 32

Gnomad AFR AF: 0.405

Gnomad AMI AF: 0.0998

Gnomad AMR AF: 0.225

Gnomad ASJ AF: 0.0384

Gnomad EAS AF: 0.114

Gnomad SAS AF: 0.0934

Gnomad FIN AF: 0.0260

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0371

Gnomad OTH AF: 0.136

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

GnomAD4 genome AF: 0.162 AC: 24652 AN: 152164 Hom.: 4010 Cov.: 32 AF XY: 0.161 AC XY: 11992 AN XY: 74406

Gnomad4 AFR AF: 0.406

Gnomad4 AMR AF: 0.226

Gnomad4 ASJ AF: 0.0384

Gnomad4 EAS AF: 0.115

Gnomad4 SAS AF: 0.0926

Gnomad4 FIN AF: 0.0260

Gnomad4 NFE AF: 0.0371

Gnomad4 OTH AF: 0.137

Alfa AF: 0.00879 Hom.: 8

Bravo AF: 0.189

Asia WGS AF: 0.141 AC: 492 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.5
Dann	Benign	0.67

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs824383; hg19: chr6-64088984;