rs904015

Positions:

• chr8-11789425-C-T

Variant summary

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

The XR_948962.4(LOC105379243):​n.44-1358G>A 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 0.313 in 151,776 control chromosomes in the GnomAD database, including 7,497 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 0.31 (7497 hom., cov: 30)
• Consequence: LOC105379243 XR_948962.4 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.357

Genes affected

LOC105379243 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.345 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379243	XR_948962.4	n.44-1358G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47432 AN: 151660 Hom.: 7496 Cov.: 30

Gnomad AFR AF: 0.287

Gnomad AMI AF: 0.337

Gnomad AMR AF: 0.261

Gnomad ASJ AF: 0.405

Gnomad EAS AF: 0.272

Gnomad SAS AF: 0.211

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.418

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.313 AC: 47445 AN: 151776 Hom.: 7497 Cov.: 30 AF XY: 0.305 AC XY: 22628 AN XY: 74156

Gnomad4 AFR AF: 0.287

Gnomad4 AMR AF: 0.260

Gnomad4 ASJ AF: 0.405

Gnomad4 EAS AF: 0.271

Gnomad4 SAS AF: 0.211

Gnomad4 FIN AF: 0.280

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.337

Alfa AF: 0.344 Hom.: 18031

Bravo AF: 0.310

Asia WGS AF: 0.223 AC: 776 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	1.8
DANN	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs904015; hg19: chr8-11646934;