rs11774700

Positions:

• chr8-117208031-T-C

Variant summary

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

The XR_007061067.1(LOC105375716):​n.560-34543A>G 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 0.259 in 152,104 control chromosomes in the GnomAD database, including 5,897 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 0.26 (5897 hom., cov: 33)
• Consequence: LOC105375716 XR_007061067.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.08

Genes affected

LOC105375716 (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 (EAS) allele frequency at 95% confidence interval = 0.445 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375716	XR_007061067.1	n.560-34543A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.259 AC: 39423 AN: 151986 Hom.: 5895 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.254

Gnomad EAS AF: 0.460

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.411

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.305

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.259 AC: 39436 AN: 152104 Hom.: 5897 Cov.: 33 AF XY: 0.265 AC XY: 19705 AN XY: 74350

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.254

Gnomad4 EAS AF: 0.460

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.411

Gnomad4 NFE AF: 0.305

Gnomad4 OTH AF: 0.263

Alfa AF: 0.274 Hom.: 1406

Bravo AF: 0.247

Asia WGS AF: 0.302 AC: 1047 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	0.19
DANN	Benign	0.34

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11774700; hg19: chr8-118220270;