rs10120476

chr9-108237036-C-T

Variant summary

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

The XR_007061722.1(LOC105376214):n.720+73630G>A 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 0.0339 in 152,202 control chromosomes in the GnomAD database, including 199 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 0.034 (199 hom., cov: 32)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0882 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376214	XR_007061722.1	n.720+73630G>A		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.720+73630G>A		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.720+73630G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0338 AC: 5134 AN: 152084 Hom.: 197 Cov.: 32

Gnomad AFR AF: 0.0906

Gnomad AMI AF: 0.00659

Gnomad AMR AF: 0.0427

Gnomad ASJ AF: 0.00634

Gnomad EAS AF: 0.0193

Gnomad SAS AF: 0.0165

Gnomad FIN AF: 0.000378

Gnomad MID AF: 0.0127

Gnomad NFE AF: 0.00670

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0339 AC: 5157 AN: 152202 Hom.: 199 Cov.: 32 AF XY: 0.0325 AC XY: 2420 AN XY: 74398

Gnomad4 AFR AF: 0.0906

Gnomad4 AMR AF: 0.0434

Gnomad4 ASJ AF: 0.00634

Gnomad4 EAS AF: 0.0193

Gnomad4 SAS AF: 0.0168

Gnomad4 FIN AF: 0.000378

Gnomad4 NFE AF: 0.00671

Gnomad4 OTH AF: 0.0284

Alfa AF: 0.0195 Hom.: 20

Bravo AF: 0.0419

Asia WGS AF: 0.0280 AC: 98 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
Cadd	Benign	5.6
Dann	Benign	0.39

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10120476; hg19: chr9-110999316;