rs13419301

Positions:

• chr2-120344996-T-C
• chr2-120344996-T-G

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

LOC105373989 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105373989	XM_047446882.1	c.357T>C	p.Asp119Asp	synonymous_variant	3/3		XP_047302838.1
		n.120344996T>C		intergenic_region

Ensembl

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

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

Gnomad4 AFR AF: 0.252

Gnomad4 AMR AF: 0.0648

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.164

Gnomad4 SAS AF: 0.219

Gnomad4 FIN AF: 0.0452

Gnomad4 NFE AF: 0.0577

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0673 Hom.: 425

Bravo AF: 0.123

Asia WGS AF: 0.241 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13419301; hg19: chr2-121102572;