rs16892482

chr8-119374142-A-G

Variant summary

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

The ENST00000670132.1(ENSG00000286282):n.265-19065T>C 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 0.0491 in 152,258 control chromosomes in the GnomAD database, including 424 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 0.049 (424 hom., cov: 32)
• Consequence: ENST00000670132.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.830

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.134 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124902009	XR_007061077.1	n.1340-19065T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000670132.1	n.265-19065T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0491 AC: 7469 AN: 152140 Hom.: 426 Cov.: 32

Gnomad AFR AF: 0.138

Gnomad AMI AF: 0.00768

Gnomad AMR AF: 0.0236

Gnomad ASJ AF: 0.0444

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0308

Gnomad FIN AF: 0.0125

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0132

Gnomad OTH AF: 0.0330

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

GnomAD4 genome AF: 0.0491 AC: 7472 AN: 152258 Hom.: 424 Cov.: 32 AF XY: 0.0469 AC XY: 3491 AN XY: 74458

Gnomad4 AFR AF: 0.137

Gnomad4 AMR AF: 0.0236

Gnomad4 ASJ AF: 0.0444

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.0296

Gnomad4 FIN AF: 0.0125

Gnomad4 NFE AF: 0.0132

Gnomad4 OTH AF: 0.0326

Alfa AF: 0.0212 Hom.: 129

Bravo AF: 0.0545

Asia WGS AF: 0.0130 AC: 45 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	3.4
Dann	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16892482; hg19: chr8-120386382;