rs2287654

chr8-47036078-T-G

Variant summary

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

The XR_928842.3(LOC105375815):n.241-5029T>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 0.103 in 152,182 control chromosomes in the GnomAD database, including 1,056 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 0.10 (1056 hom., cov: 32)
• Consequence: LOC105375815 XR_928842.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

Genes affected

LOC105375815 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105375815	XR_928842.3	n.241-5029T>G		intron_variant, non_coding_transcript_variant
LOC105375815	XR_928841.3	n.240+6836T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.104 AC: 15749 AN: 152064 Hom.: 1058 Cov.: 32

Gnomad AFR AF: 0.0277

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.0855

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.131

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.176

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.103 AC: 15750 AN: 152182 Hom.: 1056 Cov.: 32 AF XY: 0.108 AC XY: 8060 AN XY: 74382

Gnomad4 AFR AF: 0.0276

Gnomad4 AMR AF: 0.0854

Gnomad4 ASJ AF: 0.127

Gnomad4 EAS AF: 0.132

Gnomad4 SAS AF: 0.243

Gnomad4 FIN AF: 0.176

Gnomad4 NFE AF: 0.128

Gnomad4 OTH AF: 0.103

Alfa AF: 0.127 Hom.: 2523

Bravo AF: 0.0920

Asia WGS AF: 0.173 AC: 600 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	3.0
Dann	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2287654; hg19: chr8-47947701;