rs1390948

chr9-73430347-T-Cchr9-73430347-T-G

Variant summary

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

The XR_001746729.1(LOC105376083):n.569A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.102 in 151,904 control chromosomes in the GnomAD database, including 2,157 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 0.10 (2157 hom., cov: 32)
• Consequence: LOC105376083 XR_001746729.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.29

Genes affected

LOC105376083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.311 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376083	XR_001746729.1	n.569A>G		non_coding_transcript_exon_variant	1/7
LOC105376084	XR_007061581.1	n.349+1189T>C		intron_variant, non_coding_transcript_variant
LOC105376084	XR_929939.1	n.329+1189T>C		intron_variant, non_coding_transcript_variant
LOC105376084	XR_929941.2	n.349+1189T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.102 AC: 15458 AN: 151786 Hom.: 2158 Cov.: 32

Gnomad AFR AF: 0.316

Gnomad AMI AF: 0.00877

Gnomad AMR AF: 0.0540

Gnomad ASJ AF: 0.0133

Gnomad EAS AF: 0.0262

Gnomad SAS AF: 0.0346

Gnomad FIN AF: 0.00330

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0149

Gnomad OTH AF: 0.0781

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

GnomAD4 genome AF: 0.102 AC: 15472 AN: 151904 Hom.: 2157 Cov.: 32 AF XY: 0.0982 AC XY: 7295 AN XY: 74280

Gnomad4 AFR AF: 0.316

Gnomad4 AMR AF: 0.0540

Gnomad4 ASJ AF: 0.0133

Gnomad4 EAS AF: 0.0253

Gnomad4 SAS AF: 0.0345

Gnomad4 FIN AF: 0.00330

Gnomad4 NFE AF: 0.0149

Gnomad4 OTH AF: 0.0778

Alfa AF: 0.00920 Hom.: 9

Bravo AF: 0.116

Asia WGS AF: 0.0630 AC: 220 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.32
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1390948; hg19: chr9-76045263;