Genetic Variant LOC101930041:n.68906217A>C (chr4-68906217-A-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 0.159 in 152,116 control chromosomes in the GnomAD database, including 2,240 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 ( 2240 hom., cov: 32)

Consequence

LOC101930041
intragenic

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.14

Publications

9 publications found

Variant links:

Genes affected

LOC101930041 (HGNC:):

LOC101930041 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.253 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101930041		n.68906217A>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000272626	ENST00000608365.2 link	n.268+658T>G		intron_variant	Intron 1 of 1	2
ENSG00000272626	ENST00000777787.1 link	n.210+658T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.159

AC:

24181

AN:

151998

Hom.:

2232

Cov.:

show subpopulations

Gnomad AFR

AF:

0.257

Gnomad AMI

AF:

0.0713

Gnomad AMR

AF:

0.109

Gnomad ASJ

AF:

0.187

Gnomad EAS

AF:

0.155

Gnomad SAS

AF:

0.140

Gnomad FIN

AF:

0.0900

Gnomad MID

AF:

0.152

Gnomad NFE

AF:

0.123

Gnomad OTH

AF:

0.166

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

GnomAD4 genome

AF:

0.159

AC:

24208

AN:

152116

Hom.:

2240

Cov.:

AF XY:

0.157

AC XY:

11646

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.257

AC:

10663

AN:

41468

American (AMR)

AF:

0.108

AC:

1656

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.187

AC:

648

AN:

3468

East Asian (EAS)

AF:

0.155

AC:

798

AN:

5162

South Asian (SAS)

AF:

0.140

AC:

673

AN:

4822

European-Finnish (FIN)

AF:

0.0900

AC:

955

AN:

10610

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.123

AC:

8364

AN:

68002

Other (OTH)

AF:

0.164

AC:

345

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1005

2010

3015

4020

5025

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

252

504

756

1008

1260

<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:

0.136

Hom.:

1763

Bravo

AF:

0.165

Asia WGS

AF:

0.153

AC:

533

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

3.7

(source)

DANN

Benign

0.27

PhyloP100

-2.1

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