rs7589138

Positions:

• chr2-120338344-T-C

Variant summary

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

The XM_047446882.1(LOC105373989):​c.142-5578T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.515 in 152,184 control chromosomes in the GnomAD database, including 22,067 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 0.51 (22067 hom., cov: 34)
• Consequence: LOC105373989 XM_047446882.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.190

Genes affected

LOC105373989 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373989	XM_047446882.1	c.142-5578T>C		intron_variant			XP_047302838.1

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78224 AN: 152066 Hom.: 22017 Cov.: 34

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.494

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.290

Gnomad SAS AF: 0.545

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.541

Gnomad NFE AF: 0.416

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.515 AC: 78338 AN: 152184 Hom.: 22067 Cov.: 34 AF XY: 0.510 AC XY: 37963 AN XY: 74400

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.495

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.289

Gnomad4 SAS AF: 0.544

Gnomad4 FIN AF: 0.344

Gnomad4 NFE AF: 0.416

Gnomad4 OTH AF: 0.504

Alfa AF: 0.438 Hom.: 30269

Bravo AF: 0.530

Asia WGS AF: 0.498 AC: 1731 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.45
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7589138; hg19: chr2-121095920;