Genetic Variant XR_927595.2:n.246+1194G>A (chr7-64290823-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 XR_927595.2(LOC105375323):n.246+1194G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.502 in 152,088 control chromosomes in the GnomAD database, including 19,934 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 0.50 ( 19934 hom., cov: 33)

Consequence

LOC105375323
XR_927595.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.39

Publications

4 publications found

Variant links:

Genes affected

LOC105375323 (HGNC:):

LOC105375323 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=-0.98).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.565 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105375323	XR_927595.2 link	n.246+1194G>A		intron_variant	Intron 1 of 3
LOC105375323	XR_927597.2 link	n.246+1194G>A		intron_variant	Intron 1 of 3

Ensembl

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

Frequencies

GnomAD3 genomes

AF:

0.503

AC:

76378

AN:

151970

Hom.:

19933

Cov.:

show subpopulations

Gnomad AFR

AF:

0.400

Gnomad AMI

AF:

0.695

Gnomad AMR

AF:

0.576

Gnomad ASJ

AF:

0.558

Gnomad EAS

AF:

0.266

Gnomad SAS

AF:

0.434

Gnomad FIN

AF:

0.618

Gnomad MID

AF:

0.506

Gnomad NFE

AF:

0.549

Gnomad OTH

AF:

0.487

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

GnomAD4 genome

AF:

0.502

AC:

76390

AN:

152088

Hom.:

19934

Cov.:

AF XY:

0.504

AC XY:

37477

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.399

AC:

16558

AN:

41492

American (AMR)

AF:

0.575

AC:

8792

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.558

AC:

1935

AN:

3470

East Asian (EAS)

AF:

0.265

AC:

1368

AN:

5154

South Asian (SAS)

AF:

0.434

AC:

2096

AN:

4830

European-Finnish (FIN)

AF:

0.618

AC:

6537

AN:

10586

Middle Eastern (MID)

AF:

0.503

AC:

148

AN:

294

European-Non Finnish (NFE)

AF:

0.549

AC:

37299

AN:

67954

Other (OTH)

AF:

0.484

AC:

1023

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1924

3848

5772

7696

9620

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

670

1340

2010

2680

3350

<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:

0.532

Hom.:

25228

Bravo

AF:

0.496

Asia WGS

AF:

0.383

AC:

1331

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

3.5

(source)

DANN

Benign

0.25

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