rs7578624

chr2-120344903-C-Gchr2-120344903-C-T

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM4 BA1

The XM_047446882.1(LOC105373989):c.264C>G(p.Tyr88Ter) 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

Genes affected

LOC105373989 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -6 ACMG points.

• PM4: Stoplost variant in XM_047446882.1 Downstream stopcodon found after 424 codons.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.205 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC105373989	XM_047446882.1	c.264C>G	p.Tyr88Ter	stop_gained	3/3

Ensembl

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

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

Gnomad4 AFR AF: 0.208

Gnomad4 AMR AF: 0.0515

Gnomad4 ASJ AF: 0.0526

Gnomad4 EAS AF: 0.160

Gnomad4 SAS AF: 0.207

Gnomad4 FIN AF: 0.0402

Gnomad4 NFE AF: 0.0391

Gnomad4 OTH AF: 0.0793

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	17
Dann	Benign	0.82

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7578624; hg19: chr2-121102479;