chr15-74577097-T-C

Position:

• chr15-74577097-T-C

Variant summary

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

The NM_006465.4(ARID3B):​c.697+3893T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0705 in 152,220 control chromosomes in the GnomAD database, including 903 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 0.071 (903 hom., cov: 31)
• Consequence: ARID3B NM_006465.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.250

Genes affected

ARID3B (HGNC:14350): (AT-rich interaction domain 3B) This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA-binding proteins. The encoded protein is homologous with two proteins that bind to the retinoblastoma gene product, and also with the mouse Bright and Drosophila dead ringer proteins. A pseudogene on chromosome 1p31 exists for this gene. Members of the ARID family have roles in embryonic patterning, cell lineage gene regulation, cell cycle control, transcriptional regulation and possibly in chromatin structure modification. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.249 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
ARID3B	NM_006465.4	c.697+3893T>C		intron_variant		ENST00000346246.10
ARID3B	NM_001307939.2	c.697+3893T>C		intron_variant
ARID3B	XR_007064418.1	n.774+3893T>C		intron_variant, non_coding_transcript_variant
ARID3B	XR_007064419.1	n.774+3893T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
ARID3B	ENST00000346246.10	c.697+3893T>C		intron_variant		1	NM_006465.4	P4
ARID3B	ENST00000622429.1	c.697+3893T>C		intron_variant		1		A2
ARID3B	ENST00000566147.1	c.-26-12723T>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.0705 AC: 10720 AN: 152102 Hom.: 897 Cov.: 31

Gnomad AFR AF: 0.0412

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.235

Gnomad SAS AF: 0.117

Gnomad FIN AF: 0.0590

Gnomad MID AF: 0.0570

Gnomad NFE AF: 0.0347

Gnomad OTH AF: 0.0837

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

GnomAD4 genome AF: 0.0705 AC: 10739 AN: 152220 Hom.: 903 Cov.: 31 AF XY: 0.0764 AC XY: 5686 AN XY: 74426

Gnomad4 AFR AF: 0.0413

Gnomad4 AMR AF: 0.256

Gnomad4 ASJ AF: 0.0320

Gnomad4 EAS AF: 0.235

Gnomad4 SAS AF: 0.117

Gnomad4 FIN AF: 0.0590

Gnomad4 NFE AF: 0.0346

Gnomad4 OTH AF: 0.0829

Alfa AF: 0.0462 Hom.: 695

Bravo AF: 0.0852

Asia WGS AF: 0.164 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.51

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: rs8041357; hg19: chr15-74869438;