8-63308096-G-T

Position:

• chr8-63308096-G-T

Variant summary

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

The XR_001745931.2(LOC105375873):​n.752+289G>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 0.346 in 151,898 control chromosomes in the GnomAD database, including 9,428 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 0.35 (9428 hom., cov: 31)
• Consequence: LOC105375873 XR_001745931.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.197

Genes affected

LOC105375873 (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 (NFE) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375873	XR_001745931.2	n.752+289G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52470 AN: 151780 Hom.: 9409 Cov.: 31

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.386

Gnomad AMR AF: 0.333

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.0415

Gnomad SAS AF: 0.363

Gnomad FIN AF: 0.308

Gnomad MID AF: 0.339

Gnomad NFE AF: 0.372

Gnomad OTH AF: 0.362

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

GnomAD4 genome AF: 0.346 AC: 52536 AN: 151898 Hom.: 9428 Cov.: 31 AF XY: 0.341 AC XY: 25311 AN XY: 74228

Gnomad4 AFR AF: 0.355

Gnomad4 AMR AF: 0.334

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.0416

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.308

Gnomad4 NFE AF: 0.372

Gnomad4 OTH AF: 0.369

Alfa AF: 0.367 Hom.: 21224

Bravo AF: 0.346

Asia WGS AF: 0.268 AC: 935 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	1.5
DANN	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7837234; hg19: chr8-64220654;