3-101693134-C-A

Variant names:

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

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).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906262	XM_047449411.1	c.343C>A	p.Gln115Lys	missense_variant	Exon 3 of 3		XP_047305367.1
LOC124906262	XM_047449412.1	c.343C>A	p.Gln115Lys	missense_variant	Exon 3 of 3		XP_047305368.1
LOC124906262	XM_047449413.1	c.343C>A	p.Gln115Lys	missense_variant	Exon 3 of 3		XP_047305369.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293268	ENST00000715156.1	c.343C>A	p.Gln115Lys	missense_variant	Exon 2 of 2			ENSP00000520357.1
ENSG00000293268	ENST00000715157.1	c.130C>A	p.Gln44Lys	missense_variant	Exon 1 of 1			ENSP00000520358.1
ENSG00000293268	ENST00000667844.1	n.730+165C>A		intron_variant	Intron 2 of 2
ENSG00000293268	ENST00000685383.1	n.697+165C>A		intron_variant	Intron 2 of 2

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 v4.3

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

Other links and lift over

dbSNP: rs112553552; hg19: chr3-101411978;