8-11789003-T-C

Position:

• chr8-11789003-T-C

Variant summary

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

The XR_948962.4(LOC105379243):​n.44-936A>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 0.213 in 151,972 control chromosomes in the GnomAD database, including 3,869 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 0.21 (3869 hom., cov: 31)
• Consequence: LOC105379243 XR_948962.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.224

Genes affected

LOC105379243 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.314 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379243	XR_948962.4	n.44-936A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32299 AN: 151852 Hom.: 3864 Cov.: 31

Gnomad AFR AF: 0.103

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.289

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.240

Gnomad SAS AF: 0.327

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.237

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.213 AC: 32318 AN: 151972 Hom.: 3869 Cov.: 31 AF XY: 0.220 AC XY: 16328 AN XY: 74270

Gnomad4 AFR AF: 0.102

Gnomad4 AMR AF: 0.290

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.240

Gnomad4 SAS AF: 0.327

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.237

Gnomad4 OTH AF: 0.215

Alfa AF: 0.175 Hom.: 680

Bravo AF: 0.204

Asia WGS AF: 0.311 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	4.0
DANN	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2645450; hg19: chr8-11646512;