rs112553552

Variant names:

• chr3-101693134-C-A
• rs112553552
• ENST00000715156.1:c.343C>A

Your query was ambiguous. Multiple possible variants found:

• chr3-101693134-C-A
• chr3-101693134-C-T

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000715156.1(ENSG00000293268):​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: ENSG00000293268 ENST00000715156.1 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

Genes affected

ENSG00000293268 (HGNC:):

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000715156.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000293268	ENST00000715156.1		c.343C>A	p.Gln115Lys	missense	Exon 2 of 2	ENSP00000520357.1	A0AAQ5BIG5
	ENSG00000293268	ENST00000715157.1		c.130C>A	p.Gln44Lys	missense	Exon 1 of 1	ENSP00000520358.1
	ENSG00000293268	ENST00000667844.1		n.730+165C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.254 AC: 28059 AN: 110460 Hom.: 0 Cov.: 50

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

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR) AF: 0.410 AC: 13372 AN: 32606

American (AMR) AF: 0.219 AC: 2354 AN: 10770

Ashkenazi Jewish (ASJ) AF: 0.176 AC: 418 AN: 2370

East Asian (EAS) AF: 0.255 AC: 919 AN: 3604

South Asian (SAS) AF: 0.258 AC: 875 AN: 3386

European-Finnish (FIN) AF: 0.215 AC: 1641 AN: 7618

Middle Eastern (MID) AF: 0.186 AC: 35 AN: 188

European-Non Finnish (NFE) AF: 0.167 AC: 7999 AN: 47908

Other (OTH) AF: 0.254 AC: 381 AN: 1502

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.112 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

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

Other links and lift over

dbSNP: rs112553552; hg19: chr3-101411978;