rs11785622

Positions:

• chr8-98305511-C-T

Variant summary

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

The XR_007061023.1(LOC105375659):​n.1085C>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 0.199 in 152,156 control chromosomes in the GnomAD database, including 3,581 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 0.20 (3581 hom., cov: 32)
• Consequence: LOC105375659 XR_007061023.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.141

Genes affected

LOC105375659 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.274 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375659	XR_007061023.1	n.1085C>T		non_coding_transcript_exon_variant	6/6

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.199 AC: 30255 AN: 152038 Hom.: 3582 Cov.: 32

Gnomad AFR AF: 0.0965

Gnomad AMI AF: 0.270

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.195

Gnomad EAS AF: 0.00269

Gnomad SAS AF: 0.182

Gnomad FIN AF: 0.237

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.277

Gnomad OTH AF: 0.200

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

GnomAD4 genome AF: 0.199 AC: 30253 AN: 152156 Hom.: 3581 Cov.: 32 AF XY: 0.196 AC XY: 14572 AN XY: 74370

Gnomad4 AFR AF: 0.0962

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.195

Gnomad4 EAS AF: 0.00270

Gnomad4 SAS AF: 0.183

Gnomad4 FIN AF: 0.237

Gnomad4 NFE AF: 0.277

Gnomad4 OTH AF: 0.198

Alfa AF: 0.229 Hom.: 548

Bravo AF: 0.185

Asia WGS AF: 0.0840 AC: 294 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	6.0
DANN	Benign	0.83

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11785622; hg19: chr8-99317739;