rs10429616

Positions:

• chr9-115756454-A-G
• chr9-115756454-A-T

Variant summary

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

The XR_930269.2(LOC105376234):​n.366+8728A>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 0.426 in 151,726 control chromosomes in the GnomAD database, including 13,911 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 0.43 (13911 hom., cov: 31)
• Consequence: LOC105376234 XR_930269.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650

Genes affected

LOC105376234 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376234	XR_930269.2	n.366+8728A>G		intron_variant, non_coding_transcript_variant
LOC105376234	XR_930268.2	n.367-3797A>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64589 AN: 151608 Hom.: 13892 Cov.: 31

Gnomad AFR AF: 0.455

Gnomad AMI AF: 0.304

Gnomad AMR AF: 0.341

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.534

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.369

Gnomad MID AF: 0.421

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.426 AC: 64627 AN: 151726 Hom.: 13911 Cov.: 31 AF XY: 0.423 AC XY: 31364 AN XY: 74108

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.340

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.535

Gnomad4 SAS AF: 0.396

Gnomad4 FIN AF: 0.369

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.453

Alfa AF: 0.430 Hom.: 18946

Bravo AF: 0.424

Asia WGS AF: 0.464 AC: 1610 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.93
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10429616; hg19: chr9-118518733;