15-74577097-T-C

Variant names:

• chr15-74577097-T-C
• rs8041357
• NM_006465.4:c.697+3893T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006465.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID3B	NM_006465.4	MANE Select	c.697+3893T>C		intron	N/A	NP_006456.1
	ARID3B	NM_001307939.2		c.697+3893T>C		intron	N/A	NP_001294868.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ARID3B	ENST00000346246.10	TSL:1 MANE Select	c.697+3893T>C		intron	N/A	ENSP00000343126.5
	ARID3B	ENST00000622429.1	TSL:1	c.697+3893T>C		intron	N/A	ENSP00000477878.1
	ARID3B	ENST00000566147.1	TSL:3	c.-26-12723T>C		intron	N/A	ENSP00000455668.1

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

African (AFR) AF: 0.0413 AC: 1716 AN: 41554

American (AMR) AF: 0.256 AC: 3911 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3472

East Asian (EAS) AF: 0.235 AC: 1212 AN: 5166

South Asian (SAS) AF: 0.117 AC: 567 AN: 4828

European-Finnish (FIN) AF: 0.0590 AC: 625 AN: 10598

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.0346 AC: 2356 AN: 68006

Other (OTH) AF: 0.0829 AC: 175 AN: 2112

Alfa AF: 0.0495 Hom.: 1895

Bravo AF: 0.0852

Asia WGS AF: 0.164 AC: 569 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.6
DANN	Benign	0.51
PhyloP100		-0.25
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs8041357; hg19: chr15-74869438;