rs3105764

Positions:

• chr8-117722487-T-A
• chr8-117722487-T-C
• chr8-117722487-T-G

Variant summary

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

The XR_007061071.1(LOC105375721):​n.9653A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.692 in 152,058 control chromosomes in the GnomAD database, including 37,724 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 0.69 (37724 hom., cov: 32)
• Consequence: LOC105375721 XR_007061071.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.11

Genes affected

LOC105375721 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.889 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375721	XR_007061071.1	n.9653A>T		non_coding_transcript_exon_variant	1/7
		n.117722487T>A		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.692 AC: 105132 AN: 151940 Hom.: 37676 Cov.: 32

Gnomad AFR AF: 0.896

Gnomad AMI AF: 0.602

Gnomad AMR AF: 0.592

Gnomad ASJ AF: 0.605

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.680

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.665

Gnomad NFE AF: 0.607

Gnomad OTH AF: 0.629

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

GnomAD4 genome AF: 0.692 AC: 105239 AN: 152058 Hom.: 37724 Cov.: 32 AF XY: 0.691 AC XY: 51309 AN XY: 74304

Gnomad4 AFR AF: 0.896

Gnomad4 AMR AF: 0.592

Gnomad4 ASJ AF: 0.605

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.680

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.607

Gnomad4 OTH AF: 0.631

Alfa AF: 0.661 Hom.: 4223

Bravo AF: 0.696

Asia WGS AF: 0.678 AC: 2355 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.23
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3105764; hg19: chr8-118734726;