rs650389

Positions:

• chr10-78706883-A-G
• chr10-78706883-A-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The XR_946100.2(LOC105378379):​n.446+37215T>C 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 0.183 in 152,190 control chromosomes in the GnomAD database, including 3,290 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 0.18 (3290 hom., cov: 32)
• Consequence: LOC105378379 XR_946100.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.77

Genes affected

LOC105378379 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.36).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.428 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105378379	XR_946100.2	n.446+37215T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27883 AN: 152072 Hom.: 3295 Cov.: 32

Gnomad AFR AF: 0.0511

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.169

Gnomad ASJ AF: 0.189

Gnomad EAS AF: 0.443

Gnomad SAS AF: 0.285

Gnomad FIN AF: 0.128

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.250

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.183 AC: 27864 AN: 152190 Hom.: 3290 Cov.: 32 AF XY: 0.179 AC XY: 13308 AN XY: 74402

Gnomad4 AFR AF: 0.0509

Gnomad4 AMR AF: 0.169

Gnomad4 ASJ AF: 0.189

Gnomad4 EAS AF: 0.443

Gnomad4 SAS AF: 0.284

Gnomad4 FIN AF: 0.128

Gnomad4 NFE AF: 0.250

Gnomad4 OTH AF: 0.164

Alfa AF: 0.233 Hom.: 7469

Bravo AF: 0.177

Asia WGS AF: 0.322 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.36
CADD	Benign	21
DANN	Benign	0.81

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs650389; hg19: chr10-80466640;