dbSNP rs2734973: LOC353009:n.29866171C>T (chr6-29866171-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The variant allele was found at a frequency of 0.109 in 152,174 control chromosomes in the GnomAD database, including 997 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 0.11 ( 997 hom., cov: 32)

Consequence

LOC353009
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.187

Publications

22 publications found

Variant links:

Genes affected

LOC353009 (HGNC:):

LOC353009 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=-0.99).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC353009		n.29866171C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290870	ENST00000647952.1 link	n.2063-8733G>A		intron_variant	Intron 1 of 3
POLR1HASP	ENST00000849679.1 link	n.587-3345G>A		intron_variant	Intron 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.109

AC:

16537

AN:

152056

Hom.:

991

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0790

Gnomad AMI

AF:

0.111

Gnomad AMR

AF:

0.133

Gnomad ASJ

AF:

0.251

Gnomad EAS

AF:

0.0552

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0760

Gnomad MID

AF:

0.123

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.132

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

GnomAD4 genome

AF:

0.109

AC:

16578

AN:

152174

Hom.:

997

Cov.:

AF XY:

0.109

AC XY:

8075

AN XY:

74388

show subpopulations

African (AFR)

AF:

0.0796

AC:

3303

AN:

41504

American (AMR)

AF:

0.132

AC:

2023

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.251

AC:

871

AN:

3468

East Asian (EAS)

AF:

0.0553

AC:

286

AN:

5172

South Asian (SAS)

AF:

0.106

AC:

509

AN:

4824

European-Finnish (FIN)

AF:

0.0760

AC:

806

AN:

10604

Middle Eastern (MID)

AF:

0.129

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8366

AN:

68002

Other (OTH)

AF:

0.130

AC:

275

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

758

1516

2275

3033

3791

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

368

552

736

920

<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:

0.118

Hom.:

2972

Bravo

AF:

0.111

Asia WGS

AF:

0.0740

AC:

259

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

3.3

(source)

DANN

Benign

0.43

PhyloP100

-0.19

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