Genetic Variant XR_926680.3:n.2192T>C (chr6-29848644-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The XR_926680.3(LOC105375010):n.2192T>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 0.161 in 152,210 control chromosomes in the GnomAD database, including 2,007 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 0.16 ( 2007 hom., cov: 33)

Consequence

LOC105375010
XR_926680.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.91

Publications

22 publications found

Variant links:

Genes affected

LOC105375010 (HGNC:):

LOC105375010 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.202 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC105375010	XR_926680.3 link	n.2192T>C	non_coding_transcript_exon_variant	Exon 3 of 3
LOC105375010	XR_926682.3 link	n.711T>C	non_coding_transcript_exon_variant	Exon 3 of 3
LOC105375010	XR_926681.2 link	n.1781-241T>C	intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24545

AN:

152092

Hom.:

2002

Cov.:

show subpopulations

Gnomad AFR

AF:

0.145

Gnomad AMI

AF:

0.183

Gnomad AMR

AF:

0.185

Gnomad ASJ

AF:

0.173

Gnomad EAS

AF:

0.213

Gnomad SAS

AF:

0.158

Gnomad FIN

AF:

0.135

Gnomad MID

AF:

0.146

Gnomad NFE

AF:

0.166

Gnomad OTH

AF:

0.153

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

GnomAD4 genome

AF:

0.161

AC:

24554

AN:

152210

Hom.:

2007

Cov.:

AF XY:

0.160

AC XY:

11913

AN XY:

74410

show subpopulations

African (AFR)

AF:

0.145

AC:

6029

AN:

41536

American (AMR)

AF:

0.185

AC:

2829

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.173

AC:

599

AN:

3466

East Asian (EAS)

AF:

0.212

AC:

1100

AN:

5180

South Asian (SAS)

AF:

0.156

AC:

753

AN:

4820

European-Finnish (FIN)

AF:

0.135

AC:

1434

AN:

10594

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.166

AC:

11266

AN:

68018

Other (OTH)

AF:

0.159

AC:

336

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1086

2172

3257

4343

5429

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

260

520

780

1040

1300

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.166

Hom.:

8748

Bravo

AF:

0.164

Asia WGS

AF:

0.261

AC:

905

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

2.1

(source)

DANN

Benign

0.45

PhyloP100

-1.9

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over