chr3-101693134-C-T

Position:

• chr3-101693134-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The XM_047449411.1(LOC124906262):​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: LOC124906262 XM_047449411.1 stop_gained
• Clinical Significance: Not reported in ClinVar
• Conservation: No conservation score assigned

Genes affected

LOC124906262 (HGNC:):

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

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

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124906262	XM_047449411.1	c.343C>T	p.Gln115*	stop_gained	3/3		XP_047305367.1
LOC124906262	XM_047449412.1	c.343C>T	p.Gln115*	stop_gained	3/3		XP_047305368.1
LOC124906262	XM_047449413.1	c.343C>T	p.Gln115*	stop_gained	3/3		XP_047305369.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PDCL3P4	ENST00000667844.1	n.730+165C>T		intron_variant
PDCL3P4	ENST00000685383.1	n.697+165C>T		intron_variant

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

Gnomad4 AFR AF: 0.0000250

Gnomad4 AMR AF: 0.00

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.0000154

Gnomad4 OTH AF: 0.00

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

Publications

LitVar

Other links and lift over

dbSNP: rs112553552; hg19: chr3-101411978;