rs10817638

Positions:

• chr9-114560262-A-G

Variant summary

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

The XR_930260.2(LOC105376229):​n.201-1521T>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 0.37 in 152,116 control chromosomes in the GnomAD database, including 10,519 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 0.37 (10519 hom., cov: 32)
• Consequence: LOC105376229 XR_930260.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.34

Genes affected

LOC105376229 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376229	XR_930260.2	n.201-1521T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.370 AC: 56245 AN: 151998 Hom.: 10511 Cov.: 32

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.404

Gnomad SAS AF: 0.368

Gnomad FIN AF: 0.329

Gnomad MID AF: 0.338

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.372

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

GnomAD4 genome AF: 0.370 AC: 56268 AN: 152116 Hom.: 10519 Cov.: 32 AF XY: 0.370 AC XY: 27504 AN XY: 74338

Gnomad4 AFR AF: 0.371

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.331

Gnomad4 EAS AF: 0.404

Gnomad4 SAS AF: 0.367

Gnomad4 FIN AF: 0.329

Gnomad4 NFE AF: 0.356

Gnomad4 OTH AF: 0.368

Alfa AF: 0.364 Hom.: 17923

Bravo AF: 0.381

Asia WGS AF: 0.366 AC: 1268 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	12
DANN	Benign	0.51

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10817638; hg19: chr9-117322542;