Genetic Variant NM_024119.3:c.562-141G>C (chr17-42109527-C-G) – ACMG Classification: Likely_benign (-2 pts)

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_024119.3(DHX58):c.562-141G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000201 in 496,368 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: not found (cov: 33)

Exomes 𝑓: 0.0000020 ( 0 hom. )

Consequence

DHX58
NM_024119.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.09

Publications

0 publications found

Variant links:

Genes affected

DHX58 (HGNC:29517): (DExH-box helicase 58) Enables double-stranded RNA binding activity; single-stranded RNA binding activity; and zinc ion binding activity. Involved in negative regulation of defense response and negative regulation of type I interferon production. Predicted to be active in cytoplasm. [provided by Alliance of Genome Resources, Apr 2022]

DHX58 links:

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ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.98).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
DHX58	NM_024119.3 link	c.562-141G>C		intron_variant	Intron 5 of 13	ENST00000251642.8	NP_077024.2	Q96C10A0A024R1Y5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
DHX58	ENST00000251642.8 link	c.562-141G>C	intron_variant	Intron 5 of 13	1	NM_024119.3	ENSP00000251642.3	Q96C10
DHX58	ENST00000413196.6 link	c.562-141G>C	intron_variant	Intron 4 of 6	5		ENSP00000416389.1	C9JG98
DHX58	ENST00000586522.5 link	n.744-141G>C	intron_variant	Intron 5 of 11	2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

AF:

0.00000201

AC:

AN:

496368

Hom.:

AF XY:

0.00000389

AC XY:

AN XY:

257198

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

13648

American (AMR)

AF:

0.00

AC:

AN:

19706

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

14194

East Asian (EAS)

AF:

0.0000330

AC:

AN:

30262

South Asian (SAS)

AF:

0.00

AC:

AN:

41778

European-Finnish (FIN)

AF:

0.00

AC:

AN:

30812

Middle Eastern (MID)

AF:

0.00

AC:

AN:

3532

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

314928

Other (OTH)

AF:

0.00

AC:

AN:

27508

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.675

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

1.8

(source)

DANN

Benign

0.44

PhyloP100

-1.1

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.10

Details are displayed if max score is > 0.2

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over