2-120338344-T-C

Variant names:

• chr2-120338344-T-C
• rs7589138
• XM_047446882.1:c.142-5578T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 publications found

Genes affected

LOC105373989 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
LOC105373989	XM_047446882.1	c.142-5578T>C		intron_variant	Intron 1 of 2		XP_047302838.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.757 AC: 31418 AN: 41524

American (AMR) AF: 0.495 AC: 7572 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3472

East Asian (EAS) AF: 0.289 AC: 1501 AN: 5188

South Asian (SAS) AF: 0.544 AC: 2622 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3642 AN: 10596

Middle Eastern (MID) AF: 0.551 AC: 162 AN: 294

European-Non Finnish (NFE) AF: 0.416 AC: 28279 AN: 67976

Other (OTH) AF: 0.504 AC: 1065 AN: 2114

Alfa AF: 0.444 Hom.: 44609

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
PhyloP100		-0.19

Splicing

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

Other links and lift over

dbSNP: rs7589138; hg19: chr2-121095920;