8-47348995-C-G

Position:

• chr8-47348995-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001080394.4(SPIDR):​c.526-47381C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,118 control chromosomes in the GnomAD database, including 40,972 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 0.73 (40972 hom., cov: 33)
• Consequence: SPIDR NM_001080394.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.06

Genes affected

SPIDR (HGNC:28971): (scaffold protein involved in DNA repair) Involved in several processes, including cellular response to camptothecin; cellular response to hydroxyurea; and regulation of double-strand break repair. Located in nuclear chromosome and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.798 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPIDR	NM_001080394.4	c.526-47381C>G		intron_variant		ENST00000297423.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPIDR	ENST00000297423.9	c.526-47381C>G		intron_variant		1	NM_001080394.4	P1

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111353 AN: 152000 Hom.: 40934 Cov.: 33

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.729

Gnomad AMR AF: 0.809

Gnomad ASJ AF: 0.710

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.586

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.631

Gnomad NFE AF: 0.735

Gnomad OTH AF: 0.752

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

GnomAD4 genome AF: 0.733 AC: 111448 AN: 152118 Hom.: 40972 Cov.: 33 AF XY: 0.729 AC XY: 54203 AN XY: 74358

Gnomad4 AFR AF: 0.720

Gnomad4 AMR AF: 0.810

Gnomad4 ASJ AF: 0.710

Gnomad4 EAS AF: 0.814

Gnomad4 SAS AF: 0.585

Gnomad4 FIN AF: 0.691

Gnomad4 NFE AF: 0.735

Gnomad4 OTH AF: 0.753

Alfa AF: 0.730 Hom.: 5013

Bravo AF: 0.744

Asia WGS AF: 0.696 AC: 2423 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.26
DANN	Benign	0.15

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

LitVar

Other links and lift over

dbSNP: rs10108778; hg19: chr8-48261562;