rs112553552

chr3-101693134-C-Achr3-101693134-C-T

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The XM_047449411.1(LOC124906262):c.343C>A(p.Gln115Lys) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. 3/3 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.25 (0 hom., cov: 50)
  • Failed GnomAD Quality Control
• Consequence: LOC124906262 XM_047449411.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

LOC124906262 (HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LOC124906262	XM_047449411.1	c.343C>A	p.Gln115Lys	missense_variant	3/3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000685383.1	n.697+165C>A		intron_variant, non_coding_transcript_variant
	ENST00000667844.1	n.730+165C>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.00 AC: 28059 AN: 110460 Hom.: 0 Cov.: 50 FAILED QC

Gnomad AFR AF: 0.410

Gnomad AMI AF: 0.195

Gnomad AMR AF: 0.218

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.215

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.167

Gnomad OTH AF: 0.252

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

GnomAD4 genome Data not reliable, filtered out with message: InbreedingCoeff AF: 0.254 AC: 28112 AN: 110556 Hom.: 0 Cov.: 50 AF XY: 0.256 AC XY: 13898 AN XY: 54296

Gnomad4 AFR AF: 0.410

Gnomad4 AMR AF: 0.219

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.258

Gnomad4 FIN AF: 0.215

Gnomad4 NFE AF: 0.167

Gnomad4 OTH AF: 0.254

Alfa AF: 0.112 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	0.30
Dann	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs112553552; hg19: chr3-101411978;