rs9332405

chr10-108428634-T-Achr10-108428634-T-Cchr10-108428634-T-G

Variant summary

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

The XR_946310.2(LOC105378477):n.613+21336A>T 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 0.299 in 151,958 control chromosomes in the GnomAD database, including 7,877 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 0.30 (7877 hom., cov: 31)
• Consequence: LOC105378477 XR_946310.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35

Genes affected

LOC105378477 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.651 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105378477	XR_946310.2	n.613+21336A>T		intron_variant, non_coding_transcript_variant
LOC105378477	XR_946308.2	n.911+21336A>T		intron_variant, non_coding_transcript_variant
LOC105378477	XR_946309.2	n.634+21336A>T		intron_variant, non_coding_transcript_variant
LOC105378477	XR_946312.2	n.912-7152A>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.299 AC: 45370 AN: 151840 Hom.: 7854 Cov.: 31

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.670

Gnomad SAS AF: 0.423

Gnomad FIN AF: 0.337

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.302

Gnomad OTH AF: 0.290

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

GnomAD4 genome AF: 0.299 AC: 45409 AN: 151958 Hom.: 7877 Cov.: 31 AF XY: 0.307 AC XY: 22787 AN XY: 74268

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.461

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.422

Gnomad4 FIN AF: 0.337

Gnomad4 NFE AF: 0.302

Gnomad4 OTH AF: 0.296

Alfa AF: 0.301 Hom.: 902

Bravo AF: 0.306

Asia WGS AF: 0.511 AC: 1778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	3.8
Dann	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9332405; hg19: chr10-110188392;