rs748212145

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_004260.4(RECQL4):​c.961G>C​(p.Gly321Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 10/13 in silico tools predict 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: 34)

Consequence

RECQL4
NM_004260.4 missense

Scores

11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -5.94
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.062307686).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
RECQL4NM_004260.4 linkc.961G>C p.Gly321Arg missense_variant 5/21 ENST00000617875.6 NP_004251.4 O94761

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
RECQL4ENST00000617875.6 linkc.961G>C p.Gly321Arg missense_variant 5/211 NM_004260.4 ENSP00000482313.2 O94761
RECQL4ENST00000621189.4 linkc.-111G>C 5_prime_UTR_variant 4/201 ENSP00000483145.1 A0A087X072
RECQL4ENST00000524998.1 linkc.481G>C p.Gly161Arg missense_variant 3/43 ENSP00000476579.1 V9GYB6

Frequencies

GnomAD3 genomes
Cov.:
34
GnomAD4 exome
Cov.:
65
GnomAD4 genome
Cov.:
34

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.072
BayesDel_addAF
Benign
-0.22
T
BayesDel_noAF
Benign
-0.55
CADD
Benign
0.0030
DANN
Benign
0.39
DEOGEN2
Benign
0.018
T
FATHMM_MKL
Benign
0.033
N
LIST_S2
Benign
0.40
T
M_CAP
Benign
0.00065
T
MetaRNN
Benign
0.062
T
PrimateAI
Benign
0.21
T
Sift4G
Benign
0.64
T
Polyphen
0.0
B
Vest4
0.11
MVP
0.73
GERP RS
-6.2
Varity_R
0.048
gMVP
0.12

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr8-145741542; API