2-120344903-C-G

Variant names:

• chr2-120344903-C-G
• rs7578624
• XM_047446882.1:c.264C>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The XM_047446882.1(LOC105373989):​c.264C>G​(p.Tyr88*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0967 in 151,760 control chromosomes in the GnomAD database, including 1,199 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 0.097 (1199 hom., cov: 31)
• Consequence: LOC105373989 XM_047446882.1 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.08
• Publications: 3 publications found

Genes affected

LOC105373989 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 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: 0.0967 AC: 14663 AN: 151644 Hom.: 1195 Cov.: 31

Gnomad AFR AF: 0.209

Gnomad AMI AF: 0.00769

Gnomad AMR AF: 0.0516

Gnomad ASJ AF: 0.0526

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.0402

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0391

Gnomad OTH AF: 0.0758

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

GnomAD4 genome AF: 0.0967 AC: 14679 AN: 151760 Hom.: 1199 Cov.: 31 AF XY: 0.0979 AC XY: 7261 AN XY: 74160

African (AFR) AF: 0.208 AC: 8625 AN: 41374

American (AMR) AF: 0.0515 AC: 787 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0526 AC: 182 AN: 3462

East Asian (EAS) AF: 0.160 AC: 809 AN: 5072

South Asian (SAS) AF: 0.207 AC: 999 AN: 4816

European-Finnish (FIN) AF: 0.0402 AC: 425 AN: 10564

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0391 AC: 2657 AN: 67880

Other (OTH) AF: 0.0793 AC: 167 AN: 2106

Alfa AF: 0.0235 Hom.: 25

Bravo AF: 0.0991

Asia WGS AF: 0.238 AC: 827 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	17
DANN	Benign	0.82
PhyloP100		1.1

Splicing

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

Other links and lift over

dbSNP: rs7578624; hg19: chr2-121102479;