8-74033276-G-T

Position:

• chr8-74033276-G-T

Variant summary

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

The XM_017013299.2(LY96):​c.384+6435G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.299 in 151,926 control chromosomes in the GnomAD database, including 9,310 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 0.30 (9310 hom., cov: 31)
• Consequence: LY96 XM_017013299.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.50

Genes affected

LY96 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LY96	XM_017013299.2	c.384+6435G>T		intron_variant
LY96	XM_017013300.2	c.294+6435G>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45392 AN: 151808 Hom.: 9269 Cov.: 31

Gnomad AFR AF: 0.585

Gnomad AMI AF: 0.171

Gnomad AMR AF: 0.286

Gnomad ASJ AF: 0.256

Gnomad EAS AF: 0.121

Gnomad SAS AF: 0.172

Gnomad FIN AF: 0.180

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.174

Gnomad OTH AF: 0.284

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

GnomAD4 genome AF: 0.299 AC: 45492 AN: 151926 Hom.: 9310 Cov.: 31 AF XY: 0.295 AC XY: 21933 AN XY: 74262

Gnomad4 AFR AF: 0.586

Gnomad4 AMR AF: 0.287

Gnomad4 ASJ AF: 0.256

Gnomad4 EAS AF: 0.121

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.180

Gnomad4 NFE AF: 0.174

Gnomad4 OTH AF: 0.284

Alfa AF: 0.257 Hom.: 903

Bravo AF: 0.323

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.16

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6995910; hg19: chr8-74945511;