8-88361098-T-G

Variant summary

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

The ENST00000665922.1(ENSG00000253553):n.193+32046T>G 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 0.203 in 151,706 control chromosomes in the GnomAD database, including 3,259 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 0.20 (3259 hom., cov: 31)
• Consequence: ENST00000665922.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.218 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375630	XR_001745653.3	n.224+32001T>G		intron_variant, non_coding_transcript_variant
LOC105375630	XR_007060996.1	n.179+32046T>G		intron_variant, non_coding_transcript_variant
LOC105375630	XR_007060997.1	n.123+32102T>G		intron_variant, non_coding_transcript_variant
LOC105375630	XR_007060998.1	n.179+32046T>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000665922.1	n.193+32046T>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.203 AC: 30824 AN: 151590 Hom.: 3245 Cov.: 31

Gnomad AFR AF: 0.210

Gnomad AMI AF: 0.357

Gnomad AMR AF: 0.219

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.0507

Gnomad SAS AF: 0.230

Gnomad FIN AF: 0.195

Gnomad MID AF: 0.163

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.203 AC: 30871 AN: 151706 Hom.: 3259 Cov.: 31 AF XY: 0.202 AC XY: 14967 AN XY: 74182

Gnomad4 AFR AF: 0.211

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.161

Gnomad4 EAS AF: 0.0506

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.195

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.225

Alfa AF: 0.170 Hom.: 754

Bravo AF: 0.204

Asia WGS AF: 0.195 AC: 675 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	0.61
Dann	Benign	0.33

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs36116061; hg19: chr8-89373327;