rs1980888

Variant names:

• chr9-89285641-G-A
• rs1980888
• XR_930101.4:n.4503C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

Genes affected

LOC105376136 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000842493.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000309620	ENST00000842493.1		n.350+2846C>T		intron	N/A
	ENSG00000309620	ENST00000842494.1		n.298+2846C>T		intron	N/A

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

African (AFR) AF: 0.190 AC: 7862 AN: 41438

American (AMR) AF: 0.348 AC: 5313 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.0707 AC: 245 AN: 3466

East Asian (EAS) AF: 0.448 AC: 2307 AN: 5144

South Asian (SAS) AF: 0.173 AC: 830 AN: 4810

European-Finnish (FIN) AF: 0.177 AC: 1865 AN: 10532

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.121 AC: 8212 AN: 67952

Other (OTH) AF: 0.168 AC: 355 AN: 2112

Alfa AF: 0.140 Hom.: 6220

Bravo AF: 0.197

Asia WGS AF: 0.317 AC: 1100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.1
DANN	Benign	0.78
PhyloP100		-0.82

Splicing

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

Other links and lift over

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