8-82696337-A-T

Variant summary

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

The ENST00000663058.1(ENSG00000254394):n.943+92707A>T 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 0.132 in 152,178 control chromosomes in the GnomAD database, including 1,407 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 0.13 (1407 hom., cov: 32)
• Consequence: ENST00000663058.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.196 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107986953	XR_001745983.1	n.84-526A>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000663058.1	n.943+92707A>T		intron_variant, non_coding_transcript_variant
	ENST00000658531.1	n.253+92707A>T		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.132 AC: 20052 AN: 152060 Hom.: 1410 Cov.: 32

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.117

Gnomad ASJ AF: 0.0984

Gnomad EAS AF: 0.00673

Gnomad SAS AF: 0.207

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.165

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.149

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

GnomAD4 genome AF: 0.132 AC: 20051 AN: 152178 Hom.: 1407 Cov.: 32 AF XY: 0.132 AC XY: 9813 AN XY: 74412

Gnomad4 AFR AF: 0.132

Gnomad4 AMR AF: 0.117

Gnomad4 ASJ AF: 0.0984

Gnomad4 EAS AF: 0.00656

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.144

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.146

Alfa AF: 0.0599 Hom.: 62

Bravo AF: 0.129

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.3
Dann	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7812601; hg19: chr8-83608572;