dbSNP rs939327: LOC105374016:n.45T>G (chr3-102667569-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_001740825.2(LOC105374016):n.45T>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0209 in 152,312 control chromosomes in the GnomAD database, including 113 homozygotes. 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 0.021 ( 113 hom., cov: 32)

Consequence

LOC105374016
XR_001740825.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.464

Variant links:

Genes affected

LOC105374016 (HGNC:):

LOC105374016 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105374016	XR_001740825.2 link	n.45T>G	non_coding_transcript_exon_variant	Exon 1 of 4
LOC105374016	XR_001740818.2 link	n.1750+61T>G	intron_variant	Intron 8 of 10
LOC105374016	XR_001740822.2 link	n.1750+61T>G	intron_variant	Intron 8 of 11

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
ENSG00000241754	ENST00000487772.2 link	n.161-294T>G	intron_variant	Intron 1 of 2	3
ENSG00000241754	ENST00000658728.1 link	n.224-294T>G	intron_variant	Intron 1 of 3
ENSG00000241754	ENST00000669553.1 link	n.223-294T>G	intron_variant	Intron 1 of 3
ENSG00000241754	ENST00000671480.1 link	n.1866+61T>G	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0209

AC:

3186

AN:

152194

Hom.:

112

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0725

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00884

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000414

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000176

Gnomad OTH

AF:

0.0153

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

GnomAD4 genome

AF:

0.0209

AC:

3190

AN:

152312

Hom.:

113

Cov.:

AF XY:

0.0197

AC XY:

1470

AN XY:

74474

show subpopulations

Gnomad4 AFR

AF:

0.0724

Gnomad4 AMR

AF:

0.00883

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000414

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.000176

Gnomad4 OTH

AF:

0.0151

Alfa

AF:

0.0178

Hom.:

Bravo

AF:

0.0237

Asia WGS

AF:

0.00202

AC:

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

DANN

Benign

0.70

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over