3-101693134-C-T

Variant names:

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

Variant summary

Our verdict is Uncertain significance. The variant received 2 ACMG points: 2P and 0B. PM2

The ENST00000715156.1(ENSG00000293268):​c.343C>T​(p.Gln115*) variant causes a stop gained change. The variant allele was found at a frequency of 0.0000138 in 145,264 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.000014 (0 hom., cov: 50)
• Consequence: ENSG00000293268 ENST00000715156.1 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned
• Publications: 1 publications found

Genes affected

ENSG00000293268 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124906262	XM_047449411.1	c.343C>T	p.Gln115*	stop_gained	Exon 3 of 3		XP_047305367.1
LOC124906262	XM_047449412.1	c.343C>T	p.Gln115*	stop_gained	Exon 3 of 3		XP_047305368.1
LOC124906262	XM_047449413.1	c.343C>T	p.Gln115*	stop_gained	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>T	p.Gln115*	stop_gained	Exon 2 of 2			ENSP00000520357.1
ENSG00000293268	ENST00000715157.1	c.130C>T	p.Gln44*	stop_gained	Exon 1 of 1			ENSP00000520358.1
ENSG00000293268	ENST00000667844.1	n.730+165C>T		intron_variant	Intron 2 of 2
ENSG00000293268	ENST00000685383.1	n.697+165C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0000138 AC: 2 AN: 145264 Hom.: 0 Cov.: 50

Gnomad AFR AF: 0.0000250

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000154

Gnomad OTH AF: 0.00

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

GnomAD4 genome AF: 0.0000138 AC: 2 AN: 145264 Hom.: 0 Cov.: 50 AF XY: 0.00 AC XY: 0 AN XY: 70874

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

African (AFR) AF: 0.0000250 AC: 1 AN: 40062

American (AMR) AF: 0.00 AC: 0 AN: 14472

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3298

East Asian (EAS) AF: 0.00 AC: 0 AN: 4922

South Asian (SAS) AF: 0.00 AC: 0 AN: 4588

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 10040

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000154 AC: 1 AN: 64748

Other (OTH) AF: 0.00 AC: 0 AN: 1990

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.000203476), which strongly suggests a high chance of mosaicism in these individuals.

Alfa AF: 0.00 Hom.: 0

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.40
DANN	Benign	0.57

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;