rs4534106

Positions:

• chr8-107777588-T-C

Variant summary

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

The XR_928527.3(LOC105375703):​n.225+888A>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 0.285 in 152,034 control chromosomes in the GnomAD database, including 6,394 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 0.28 (6394 hom., cov: 32)
• Consequence: LOC105375703 XR_928527.3 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.185

Genes affected

LOC105375703 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.323 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375703	XR_928527.3	n.225+888A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.285 AC: 43237 AN: 151916 Hom.: 6383 Cov.: 32

Gnomad AFR AF: 0.239

Gnomad AMI AF: 0.181

Gnomad AMR AF: 0.280

Gnomad ASJ AF: 0.319

Gnomad EAS AF: 0.138

Gnomad SAS AF: 0.337

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.229

Gnomad NFE AF: 0.319

Gnomad OTH AF: 0.280

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

GnomAD4 genome AF: 0.285 AC: 43279 AN: 152034 Hom.: 6394 Cov.: 32 AF XY: 0.281 AC XY: 20904 AN XY: 74324

Gnomad4 AFR AF: 0.239

Gnomad4 AMR AF: 0.281

Gnomad4 ASJ AF: 0.319

Gnomad4 EAS AF: 0.137

Gnomad4 SAS AF: 0.336

Gnomad4 FIN AF: 0.296

Gnomad4 NFE AF: 0.319

Gnomad4 OTH AF: 0.280

Alfa AF: 0.313 Hom.: 6285

Bravo AF: 0.277

Asia WGS AF: 0.271 AC: 943 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	6.8
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4534106; hg19: chr8-108789816;