rs2989579

Positions:

• chr9-78370826-T-C
• chr9-78370826-T-G

Variant summary

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

The XR_001746759.2(LOC107987083):​n.1048+12174T>C 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 0.219 in 152,206 control chromosomes in the GnomAD database, including 4,018 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 0.22 (4018 hom., cov: 33)
• Consequence: LOC107987083 XR_001746759.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.36

Genes affected

LOC107987083 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.256 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC107987083	XR_001746759.2	n.1048+12174T>C		intron_variant, non_coding_transcript_variant
LOC107987083	XR_001746760.2	n.1048+12174T>C		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33252 AN: 152088 Hom.: 4014 Cov.: 33

Gnomad AFR AF: 0.141

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.280

Gnomad EAS AF: 0.0550

Gnomad SAS AF: 0.191

Gnomad FIN AF: 0.311

Gnomad MID AF: 0.304

Gnomad NFE AF: 0.259

Gnomad OTH AF: 0.219

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

GnomAD4 genome AF: 0.219 AC: 33272 AN: 152206 Hom.: 4018 Cov.: 33 AF XY: 0.218 AC XY: 16235 AN XY: 74404

Gnomad4 AFR AF: 0.141

Gnomad4 AMR AF: 0.229

Gnomad4 ASJ AF: 0.280

Gnomad4 EAS AF: 0.0551

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.311

Gnomad4 NFE AF: 0.259

Gnomad4 OTH AF: 0.216

Alfa AF: 0.231 Hom.: 2788

Bravo AF: 0.211

Asia WGS AF: 0.116 AC: 403 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	2.5
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2989579; hg19: chr9-80985742; COSMIC: COSV60363064;