rs1675306

chr9-90934941-A-Cchr9-90934941-A-Gchr9-90934941-A-T

Variant summary

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

The XR_001746828.2(LOC105379829):n.243-2885T>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 0.944 in 152,312 control chromosomes in the GnomAD database, including 68,168 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 0.94 (68168 hom., cov: 34)
• Consequence: LOC105379829 XR_001746828.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.355

Genes affected

LOC105379829 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.983 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105379829	XR_001746828.2	n.243-2885T>G		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.944 AC: 143729 AN: 152194 Hom.: 68133 Cov.: 34

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.965

Gnomad AMR AF: 0.922

Gnomad ASJ AF: 0.991

Gnomad EAS AF: 0.897

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.995

Gnomad MID AF: 0.972

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.957

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

GnomAD4 genome AF: 0.944 AC: 143819 AN: 152312 Hom.: 68168 Cov.: 34 AF XY: 0.943 AC XY: 70220 AN XY: 74482

Gnomad4 AFR AF: 0.869

Gnomad4 AMR AF: 0.922

Gnomad4 ASJ AF: 0.991

Gnomad4 EAS AF: 0.897

Gnomad4 SAS AF: 0.927

Gnomad4 FIN AF: 0.995

Gnomad4 NFE AF: 0.989

Gnomad4 OTH AF: 0.957

Alfa AF: 0.984 Hom.: 52105

Bravo AF: 0.941

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.73
Dann	Benign	0.60

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1675306; hg19: chr9-93697223;