rs1980888

chr9-89285641-G-A

Variant summary

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

The XR_930101.4(LOC105376136):n.4503C>T 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 0.178 in 151,934 control chromosomes in the GnomAD database, including 3,266 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 0.18 (3266 hom., cov: 32)
• Consequence: LOC105376136 XR_930101.4 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

Genes affected

LOC105376136 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.433 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105376136	XR_930101.4	n.4503C>T		non_coding_transcript_exon_variant	3/3

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27042 AN: 151816 Hom.: 3244 Cov.: 32

Gnomad AFR AF: 0.189

Gnomad AMI AF: 0.0932

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.0707

Gnomad EAS AF: 0.449

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.121

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.178 AC: 27100 AN: 151934 Hom.: 3266 Cov.: 32 AF XY: 0.186 AC XY: 13794 AN XY: 74218

Gnomad4 AFR AF: 0.190

Gnomad4 AMR AF: 0.348

Gnomad4 ASJ AF: 0.0707

Gnomad4 EAS AF: 0.448

Gnomad4 SAS AF: 0.173

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.121

Gnomad4 OTH AF: 0.168

Alfa AF: 0.129 Hom.: 3264

Bravo AF: 0.197

Asia WGS AF: 0.317 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	1.1
Dann	Benign	0.78

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1980888; hg19: chr9-91900556; COSMIC: COSV60375277;