rs73511817

chr9-108383745-C-A

Variant summary

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

The XR_007061722.1(LOC105376214):n.326-8149G>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 0.0421 in 152,028 control chromosomes in the GnomAD database, including 185 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 0.042 (185 hom., cov: 32)
• Consequence: LOC105376214 XR_007061722.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.84

Genes affected

LOC105376214 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.45).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0688 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376214	XR_007061722.1	n.326-8149G>T		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746881.2	n.326-8149G>T		intron_variant, non_coding_transcript_variant
LOC105376214	XR_001746882.2	n.326-8149G>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0421 AC: 6394 AN: 151910 Hom.: 185 Cov.: 32

Gnomad AFR AF: 0.0686

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0372

Gnomad ASJ AF: 0.0525

Gnomad EAS AF: 0.000577

Gnomad SAS AF: 0.0748

Gnomad FIN AF: 0.0204

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0313

Gnomad OTH AF: 0.0411

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

GnomAD4 genome AF: 0.0421 AC: 6401 AN: 152028 Hom.: 185 Cov.: 32 AF XY: 0.0429 AC XY: 3186 AN XY: 74312

Gnomad4 AFR AF: 0.0686

Gnomad4 AMR AF: 0.0371

Gnomad4 ASJ AF: 0.0525

Gnomad4 EAS AF: 0.000771

Gnomad4 SAS AF: 0.0752

Gnomad4 FIN AF: 0.0204

Gnomad4 NFE AF: 0.0313

Gnomad4 OTH AF: 0.0407

Alfa AF: 0.0349 Hom.: 8

Bravo AF: 0.0432

Asia WGS AF: 0.0280 AC: 98 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.45
Cadd	Benign	21
Dann	Benign	0.55

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs73511817; hg19: chr9-111146025;