rs760575376

chr8-144513210-GT-G

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP6_Moderate

The NM_004260.4(RECQL4):c.2463+7del variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0024 (0 hom., cov: 20)
  • Exomes 𝑓: 0.00081 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: RECQL4 NM_004260.4 splice_region, intron
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: -3.11

Genes affected

RECQL4 (HGNC:9949): (RecQ like helicase 4) The protein encoded by this gene is a DNA helicase that belongs to the RecQ helicase family. DNA helicases unwind double-stranded DNA into single-stranded DNAs and may modulate chromosome segregation. This gene is predominantly expressed in thymus and testis. Mutations in this gene are associated with Rothmund-Thomson, RAPADILINO and Baller-Gerold syndromes. [provided by RefSeq, Jan 2010]

(HGNC:):

ACMG classification

Verdict is Likely_benign. Variant got -2 ACMG points.

• BP6: Variant 8-144513210-GT-G is Benign according to our data. Variant chr8-144513210-GT-G is described in ClinVar as [Benign]. Clinvar id is 239733.Status of the report is criteria_provided_single_submitter, 1 stars. Variant chr8-144513210-GT-G is described in Lovd as [Likely_benign].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
RECQL4	NM_004260.4	c.2463+7del		splice_region_variant, intron_variant		ENST00000617875.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
RECQL4	ENST00000617875.6	c.2463+7del		splice_region_variant, intron_variant		1	NM_004260.4	P1
RECQL4	ENST00000621189.4	c.1392+7del		splice_region_variant, intron_variant		1
	ENST00000580385.1	n.271+374del		intron_variant, non_coding_transcript_variant		3
RECQL4	ENST00000534626.6	c.635-73del		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00 AC: 303 AN: 125398 Hom.: 0 Cov.: 20 FAILED QC

Gnomad AFR AF: 0.00602

Gnomad AMI AF: 0.00380

Gnomad AMR AF: 0.00112

Gnomad ASJ AF: 0.000999

Gnomad EAS AF: 0.000722

Gnomad SAS AF: 0.000527

Gnomad FIN AF: 0.000619

Gnomad MID AF: 0.00394

Gnomad NFE AF: 0.00102

Gnomad OTH AF: 0.00176

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.000813 AC: 1065 AN: 1310156 Hom.: 0 Cov.: 40 AF XY: 0.00104 AC XY: 668 AN XY: 641164

Gnomad4 AFR exome AF: 0.00155

Gnomad4 AMR exome AF: 0.00365

Gnomad4 ASJ exome AF: 0.00252

Gnomad4 EAS exome AF: 0.00113

Gnomad4 SAS exome AF: 0.00282

Gnomad4 FIN exome AF: 0.00110

Gnomad4 NFE exome AF: 0.000528

Gnomad4 OTH exome AF: 0.000347

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.00242 AC: 303 AN: 125444 Hom.: 0 Cov.: 20 AF XY: 0.00235 AC XY: 142 AN XY: 60382

Gnomad4 AFR AF: 0.00603

Gnomad4 AMR AF: 0.00112

Gnomad4 ASJ AF: 0.000999

Gnomad4 EAS AF: 0.000724

Gnomad4 SAS AF: 0.000265

Gnomad4 FIN AF: 0.000619

Gnomad4 NFE AF: 0.00102

Gnomad4 OTH AF: 0.00174

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

Baller-Gerold syndrome Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Aug 17, 2023

- -

Computational scores

Source: dbNSFP v4.3

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.060		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs760575376; hg19: chr8-145738593; COSMIC: COSV52882819; COSMIC: COSV52882819;