XM_047446882.1:c.357T>C

Variant names:

• chr2-120344996-T-C
• rs13419301
• XM_047446882.1:c.357T>C

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The XM_047446882.1(LOC105373989):​c.357T>C​(p.Asp119Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 149,154 control chromosomes in the GnomAD database, including 1,693 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 (1693 hom., cov: 31)
• Consequence: LOC105373989 XM_047446882.1 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483
• Publications: 2 publications found

Genes affected

LOC105373989 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.49).
• BP7: Synonymous conserved (PhyloP=-0.483 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.248 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.121 AC: 17996 AN: 149036 Hom.: 1692 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.0278

Gnomad AMR AF: 0.0650

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.165

Gnomad SAS AF: 0.220

Gnomad FIN AF: 0.0452

Gnomad MID AF: 0.118

Gnomad NFE AF: 0.0577

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.121 AC: 18013 AN: 149154 Hom.: 1693 Cov.: 31 AF XY: 0.121 AC XY: 8818 AN XY: 72816

African (AFR) AF: 0.252 AC: 10173 AN: 40406

American (AMR) AF: 0.0648 AC: 980 AN: 15118

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 426 AN: 3454

East Asian (EAS) AF: 0.164 AC: 792 AN: 4826

South Asian (SAS) AF: 0.219 AC: 1024 AN: 4668

European-Finnish (FIN) AF: 0.0452 AC: 460 AN: 10184

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.0577 AC: 3878 AN: 67226

Other (OTH) AF: 0.106 AC: 220 AN: 2080

Alfa AF: 0.0747 Hom.: 743

Bravo AF: 0.123

Asia WGS AF: 0.241 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.49
CADD	Benign	16
DANN	Benign	0.58
PhyloP100		-0.48

Splicing

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

Other links and lift over

dbSNP: rs13419301; hg19: chr2-121102572;