dbSNP rs979037: LOC101928331:n.14458A>C (chr6-14471294-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_007059467.1(LOC101928331):n.14458A>C 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 0.52 in 152,092 control chromosomes in the GnomAD database, including 21,696 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 0.52 ( 21696 hom., cov: 32)

Consequence

LOC101928331
XR_007059467.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.72

Variant links:

Genes affected

LOC101928331 (HGNC:):

LOC101928331 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.58).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.708 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC101928331	XR_007059467.1 link	n.14458A>C	non_coding_transcript_exon_variant	Exon 2 of 2
LOC101928331	XR_001743994.3 link	n.296-26763A>C	intron_variant	Intron 1 of 2
LOC101928331	XR_001743997.3 link	n.139-26763A>C	intron_variant	Intron 1 of 3
LOC101928331	XR_001743999.3 link	n.139-26763A>C	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286277	ENST00000666857.1 link	n.393-26763A>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.519

AC:

78939

AN:

151972

Hom.:

21652

Cov.:

show subpopulations

Gnomad AFR

AF:

0.660

Gnomad AMI

AF:

0.580

Gnomad AMR

AF:

0.553

Gnomad ASJ

AF:

0.387

Gnomad EAS

AF:

0.728

Gnomad SAS

AF:

0.685

Gnomad FIN

AF:

0.369

Gnomad MID

AF:

0.446

Gnomad NFE

AF:

0.429

Gnomad OTH

AF:

0.492

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

GnomAD4 genome

AF:

0.520

AC:

79050

AN:

152092

Hom.:

21696

Cov.:

AF XY:

0.521

AC XY:

38716

AN XY:

74340

show subpopulations

Gnomad4 AFR

AF:

0.660

Gnomad4 AMR

AF:

0.554

Gnomad4 ASJ

AF:

0.387

Gnomad4 EAS

AF:

0.728

Gnomad4 SAS

AF:

0.686

Gnomad4 FIN

AF:

0.369

Gnomad4 NFE

AF:

0.429

Gnomad4 OTH

AF:

0.494

Alfa

AF:

0.396

Hom.:

1706

Bravo

AF:

0.537

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

DANN

Benign

0.89

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