Genetic Variant LOC387770:n.49856729T>C (chr11-49856729-T-C) – 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 0.662 in 151,984 control chromosomes in the GnomAD database, including 33,831 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 0.66 ( 33831 hom., cov: 32)

Consequence

LOC387770
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.37

Publications

5 publications found

Variant links:

Genes affected

LOC387770 (HGNC:):

LOC387770 links:

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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=-1.0).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.751 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC387770		n.49856729T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000255550	ENST00000532033.1 link	n.158+990A>G		intron_variant	Intron 2 of 3	6
ENSG00000288177	ENST00000672270.1 link	n.292+4220T>C		intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.662

AC:

100610

AN:

151866

Hom.:

33804

Cov.:

show subpopulations

Gnomad AFR

AF:

0.568

Gnomad AMI

AF:

0.720

Gnomad AMR

AF:

0.762

Gnomad ASJ

AF:

0.754

Gnomad EAS

AF:

0.703

Gnomad SAS

AF:

0.766

Gnomad FIN

AF:

0.645

Gnomad MID

AF:

0.665

Gnomad NFE

AF:

0.683

Gnomad OTH

AF:

0.708

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

GnomAD4 genome

AF:

0.662

AC:

100679

AN:

151984

Hom.:

33831

Cov.:

AF XY:

0.664

AC XY:

49332

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.568

AC:

23531

AN:

41432

American (AMR)

AF:

0.763

AC:

11664

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.754

AC:

2615

AN:

3466

East Asian (EAS)

AF:

0.703

AC:

3611

AN:

5138

South Asian (SAS)

AF:

0.766

AC:

3690

AN:

4816

European-Finnish (FIN)

AF:

0.645

AC:

6811

AN:

10564

Middle Eastern (MID)

AF:

0.667

AC:

196

AN:

294

European-Non Finnish (NFE)

AF:

0.683

AC:

46401

AN:

67958

Other (OTH)

AF:

0.713

AC:

1506

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1724

3448

5173

6897

8621

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

798

1596

2394

3192

3990

<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:

0.664

Hom.:

4201

Bravo

AF:

0.665

Asia WGS

AF:

0.753

AC:

2620

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.81

(source)

DANN

Benign

0.35

PhyloP100

-1.4

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