Variant 17-75630842-G-GTGTGT details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_004259.7(RECQL5):c.1586-6_1586-5insACACA variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000061 in 1,147,244 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 21)

Exomes 𝑓: 0.0000061 ( 1 hom. )

Consequence

RECQL5
NM_004259.7 splice_region, intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.258

Variant links:

Genes affected

RECQL5 (HGNC:9950): (RecQ like helicase 5) The protein encoded by this gene is a helicase that is important for genome stability. The encoded protein also prevents aberrant homologous recombination by displacing RAD51 from ssDNA. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2011]

RECQL5 links:

RECQL5 (HGNC:):

RECQL5 links:

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RECQL5	NM_004259.7 linkuse as main transcript	c.1586-6_1586-5insACACA		splice_region_variant, intron_variant		ENST00000317905.10	NP_004250.4	O94762-1A0A024R8M9Q8WYH5

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	UniProt
RECQL5	ENST00000317905.10 linkuse as main transcript	c.1586-6_1586-5insACACA	splice_region_variant, intron_variant	1	NM_004259.7	ENSP00000317636.5	O94762-1
RECQL5	ENST00000423245.6 linkuse as main transcript	c.1505-6_1505-5insACACA	splice_region_variant, intron_variant	1		ENSP00000394820.2	O94762-4
RECQL5	ENST00000443199.6 linkuse as main transcript	n.1122-6_1122-5insACACA	splice_region_variant, intron_variant	1
RECQL5	ENST00000580707.1 linkuse as main transcript	c.53-6_53-5insACACA	splice_region_variant, intron_variant	3		ENSP00000463701.1	J3QLU0

Frequencies

GnomAD3 genomes

Cov.:

GnomAD3 exomes

AF:

0.0000348

AC:

AN:

57474

Hom.:

AF XY:

0.0000691

AC XY:

AN XY:

28946

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000861

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00000610

AC:

AN:

1147244

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

561690

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.0000863

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00000438

Gnomad4 OTH exome

AF:

0.0000213

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over