rs2818309

chr9-118977520-C-T

Variant summary

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

The XR_001746918.2(LOC101928849):n.1046+84C>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 0.591 in 151,826 control chromosomes in the GnomAD database, including 27,956 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 0.59 (27956 hom., cov: 32)
• Consequence: LOC101928849 XR_001746918.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

Genes affected

LOC101928849 (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 (AMR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC101928849	XR_001746918.2	n.1046+84C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.591 AC: 89671 AN: 151708 Hom.: 27952 Cov.: 32

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.816

Gnomad AMR AF: 0.695

Gnomad ASJ AF: 0.601

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.495

Gnomad FIN AF: 0.651

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.581

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

GnomAD4 genome AF: 0.591 AC: 89689 AN: 151826 Hom.: 27956 Cov.: 32 AF XY: 0.591 AC XY: 43838 AN XY: 74220

Gnomad4 AFR AF: 0.381

Gnomad4 AMR AF: 0.695

Gnomad4 ASJ AF: 0.601

Gnomad4 EAS AF: 0.602

Gnomad4 SAS AF: 0.495

Gnomad4 FIN AF: 0.651

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.578

Alfa AF: 0.646 Hom.: 5554

Bravo AF: 0.594

Asia WGS AF: 0.563 AC: 1960 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	1.5
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: rs2818309; hg19: chr9-121739798;