rs1891983

Variant names:

• chr9-135242467-C-T
• rs1891983
• XR_001746966.2:n.5122G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XR_001746966.2(LOC107987138):​n.5122G>A 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 0.117 in 152,160 control chromosomes in the GnomAD database, including 1,261 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 0.12 (1261 hom., cov: 32)
• Consequence: LOC107987138 XR_001746966.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.07
• Publications: 1 publications found

Genes affected

LOC107987138 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.117 AC: 17718 AN: 152042 Hom.: 1259 Cov.: 32

Gnomad AFR AF: 0.196

Gnomad AMI AF: 0.257

Gnomad AMR AF: 0.0787

Gnomad ASJ AF: 0.0870

Gnomad EAS AF: 0.000386

Gnomad SAS AF: 0.0398

Gnomad FIN AF: 0.0968

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0943

Gnomad OTH AF: 0.100

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

GnomAD4 genome AF: 0.117 AC: 17740 AN: 152160 Hom.: 1261 Cov.: 32 AF XY: 0.113 AC XY: 8406 AN XY: 74388

African (AFR) AF: 0.196 AC: 8141 AN: 41498

American (AMR) AF: 0.0786 AC: 1202 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0870 AC: 302 AN: 3472

East Asian (EAS) AF: 0.000387 AC: 2 AN: 5166

South Asian (SAS) AF: 0.0396 AC: 191 AN: 4818

European-Finnish (FIN) AF: 0.0968 AC: 1026 AN: 10594

Middle Eastern (MID) AF: 0.0476 AC: 14 AN: 294

European-Non Finnish (NFE) AF: 0.0943 AC: 6416 AN: 68010

Other (OTH) AF: 0.100 AC: 212 AN: 2112

Alfa AF: 0.0966 Hom.: 1097

Bravo AF: 0.121

Asia WGS AF: 0.0380 AC: 133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.68
DANN	Benign	0.45
PhyloP100		-2.1

Splicing

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

Other links and lift over

dbSNP: rs1891983; hg19: chr9-138134313;