rs10875976

Variant names:

• chr12-49832684-G-A
• rs10875976
• ENST00000548872.5:n.356+3601G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000548872.5(BCDIN3D-AS1):​n.356+3601G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 152,028 control chromosomes in the GnomAD database, including 13,673 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 0.41 (13673 hom., cov: 32)
• Consequence: BCDIN3D-AS1 ENST00000548872.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.181
• Publications: 17 publications found

Genes affected

BCDIN3D-AS1 (HGNC:44113): (BCDIN3D antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000548872.5. 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
	BCDIN3D-AS1	NR_027499.1		n.355+3601G>A		intron	N/A
	BCDIN3D-AS1	NR_027500.1		n.351+3601G>A		intron	N/A
	BCDIN3D-AS1	NR_027501.1		n.351+3601G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BCDIN3D-AS1	ENST00000548872.5	TSL:1	n.356+3601G>A		intron	N/A
	BCDIN3D-AS1	ENST00000549124.2	TSL:3	n.341+3601G>A		intron	N/A
	BCDIN3D-AS1	ENST00000670504.2		n.215+3601G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.415 AC: 62986 AN: 151908 Hom.: 13669 Cov.: 32

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.522

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.507

Gnomad MID AF: 0.379

Gnomad NFE AF: 0.483

Gnomad OTH AF: 0.408

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

GnomAD4 genome AF: 0.414 AC: 62992 AN: 152028 Hom.: 13673 Cov.: 32 AF XY: 0.411 AC XY: 30546 AN XY: 74306

African (AFR) AF: 0.311 AC: 12875 AN: 41454

American (AMR) AF: 0.323 AC: 4939 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.522 AC: 1811 AN: 3470

East Asian (EAS) AF: 0.326 AC: 1684 AN: 5158

South Asian (SAS) AF: 0.444 AC: 2145 AN: 4826

European-Finnish (FIN) AF: 0.507 AC: 5357 AN: 10562

Middle Eastern (MID) AF: 0.380 AC: 111 AN: 292

European-Non Finnish (NFE) AF: 0.483 AC: 32803 AN: 67962

Other (OTH) AF: 0.404 AC: 855 AN: 2116

Alfa AF: 0.445 Hom.: 40532

Bravo AF: 0.390

Asia WGS AF: 0.359 AC: 1250 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.4
DANN	Benign	0.72
PhyloP100		0.18

Splicing

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

Other links and lift over

dbSNP: rs10875976; hg19: chr12-50226467;