8-131292261-T-C

Position:

• chr8-131292261-T-C

Variant summary

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

The XR_007061183.1(LOC105375760):​n.634-1648T>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 0.604 in 151,230 control chromosomes in the GnomAD database, including 27,960 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 0.60 (27960 hom., cov: 29)
• Consequence: LOC105375760 XR_007061183.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.14

Genes affected

LOC105375760 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375760	XR_007061183.1	n.634-1648T>C		intron_variant, non_coding_transcript_variant
LOC105375760	XR_928653.3	n.496-1648T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.604 AC: 91253 AN: 151114 Hom.: 27928 Cov.: 29

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.515

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.399

Gnomad SAS AF: 0.539

Gnomad FIN AF: 0.555

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.597

Gnomad OTH AF: 0.560

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

GnomAD4 genome AF: 0.604 AC: 91342 AN: 151230 Hom.: 27960 Cov.: 29 AF XY: 0.596 AC XY: 44055 AN XY: 73908

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.516

Gnomad4 ASJ AF: 0.524

Gnomad4 EAS AF: 0.398

Gnomad4 SAS AF: 0.539

Gnomad4 FIN AF: 0.555

Gnomad4 NFE AF: 0.597

Gnomad4 OTH AF: 0.559

Alfa AF: 0.588 Hom.: 53166

Bravo AF: 0.601

Asia WGS AF: 0.463 AC: 1610 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.12
DANN	Benign	0.70

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10102742; hg19: chr8-132304508;