8-82161594-C-T

Position:

• chr8-82161594-C-T

Variant summary

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

The ENST00000659043.1(ENSG00000254394):​n.145+87870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.62 in 152,028 control chromosomes in the GnomAD database, including 31,115 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 0.62 (31115 hom., cov: 32)
• Consequence: ENSG00000254394 ENST00000659043.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.173

Genes affected

ENSG00000254394 (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 (NFE) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375930	XR_929113.2	n.326-343C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000254394	ENST00000659043.1	n.145+87870C>T		intron_variant
ENSG00000254394	ENST00000663058.1	n.392+87870C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94213 AN: 151912 Hom.: 31113 Cov.: 32

Gnomad AFR AF: 0.375

Gnomad AMI AF: 0.745

Gnomad AMR AF: 0.709

Gnomad ASJ AF: 0.672

Gnomad EAS AF: 0.599

Gnomad SAS AF: 0.686

Gnomad FIN AF: 0.686

Gnomad MID AF: 0.630

Gnomad NFE AF: 0.731

Gnomad OTH AF: 0.657

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

GnomAD4 genome AF: 0.620 AC: 94223 AN: 152028 Hom.: 31115 Cov.: 32 AF XY: 0.623 AC XY: 46264 AN XY: 74296

Gnomad4 AFR AF: 0.374

Gnomad4 AMR AF: 0.708

Gnomad4 ASJ AF: 0.672

Gnomad4 EAS AF: 0.600

Gnomad4 SAS AF: 0.686

Gnomad4 FIN AF: 0.686

Gnomad4 NFE AF: 0.731

Gnomad4 OTH AF: 0.651

Alfa AF: 0.708 Hom.: 18919

Bravo AF: 0.613

Asia WGS AF: 0.568 AC: 1978 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.8
DANN	Benign	0.75

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13264970; hg19: chr8-83073829;