rs6838908

chr4-13587588-A-Gchr4-13587588-A-T

Variant summary

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

The NM_148894.3(BOD1L1):c.8353+111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.795 in 765,992 control chromosomes in the GnomAD database, including 248,364 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 0.70 (40956 hom., cov: 31)
  • Exomes 𝑓: 0.82 (207408 hom.)
• Consequence: BOD1L1 NM_148894.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.697

Genes affected

BOD1L1 (HGNC:31792): (biorientation of chromosomes in cell division 1 like 1) Predicted to enable protein phosphatase 2A binding activity and protein phosphatase inhibitor activity. Involved in cellular response to DNA damage stimulus and replication fork processing. Located in 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.938 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BOD1L1	NM_148894.3	c.8353+111T>C		intron_variant		ENST00000040738.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BOD1L1	ENST00000040738.10	c.8353+111T>C		intron_variant		1	NM_148894.3	P2
BOD1L1	ENST00000507943.2	c.8353+111T>C		intron_variant		3		A2
BOD1L1	ENST00000511119.1	n.1803+111T>C		intron_variant, non_coding_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.703 AC: 106766 AN: 151974 Hom.: 40934 Cov.: 31

Gnomad AFR AF: 0.371

Gnomad AMI AF: 0.914

Gnomad AMR AF: 0.826

Gnomad ASJ AF: 0.806

Gnomad EAS AF: 0.960

Gnomad SAS AF: 0.872

Gnomad FIN AF: 0.848

Gnomad MID AF: 0.766

Gnomad NFE AF: 0.813

Gnomad OTH AF: 0.720

GnomAD4 exome AF: 0.818 AC: 501867 AN: 613900 Hom.: 207408 AF XY: 0.821 AC XY: 263839 AN XY: 321504

Gnomad4 AFR exome AF: 0.365

Gnomad4 AMR exome AF: 0.870

Gnomad4 ASJ exome AF: 0.819

Gnomad4 EAS exome AF: 0.960

Gnomad4 SAS exome AF: 0.867

Gnomad4 FIN exome AF: 0.851

Gnomad4 NFE exome AF: 0.813

Gnomad4 OTH exome AF: 0.799

GnomAD4 genome AF: 0.702 AC: 106817 AN: 152092 Hom.: 40956 Cov.: 31 AF XY: 0.710 AC XY: 52833 AN XY: 74384

Gnomad4 AFR AF: 0.370

Gnomad4 AMR AF: 0.826

Gnomad4 ASJ AF: 0.806

Gnomad4 EAS AF: 0.960

Gnomad4 SAS AF: 0.873

Gnomad4 FIN AF: 0.848

Gnomad4 NFE AF: 0.813

Gnomad4 OTH AF: 0.723

Alfa AF: 0.743 Hom.: 5516

Bravo AF: 0.687

Asia WGS AF: 0.880 AC: 3059 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	2.0
Dann	Benign	0.77

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: rs6838908; hg19: chr4-13589212;