ENST00000453174.7:n.742+3318A>G

Variant names:

• chr10-79925306-A-G
• rs2256573
• ENST00000453174.7:n.742+3318A>G

Variant summary

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

The ENST00000453174.7(ENSG00000283913):​n.742+3318A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.594 in 151,854 control chromosomes in the GnomAD database, including 27,625 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 0.59 (27625 hom., cov: 32)
• Consequence: ENSG00000283913 ENST00000453174.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.62
• Publications: 8 publications found

Genes affected

ENSG00000283913 (HGNC:):

BMS1P21 (HGNC:51604): (BMS1 pseudogene 21)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.744 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453174.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMS1P21	NR_033857.1		n.742+3318A>G		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283913	ENST00000453174.7	TSL:2	n.742+3318A>G		intron	N/A
	ENSG00000283913	ENST00000818194.1		n.633+17450A>G		intron	N/A
	ENSG00000283913	ENST00000818195.1		n.829-6420A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.594 AC: 90140 AN: 151736 Hom.: 27572 Cov.: 32

Gnomad AFR AF: 0.751

Gnomad AMI AF: 0.557

Gnomad AMR AF: 0.582

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.505

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.530

Gnomad MID AF: 0.592

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.590

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

GnomAD4 genome AF: 0.594 AC: 90263 AN: 151854 Hom.: 27625 Cov.: 32 AF XY: 0.594 AC XY: 44077 AN XY: 74180

African (AFR) AF: 0.751 AC: 31120 AN: 41440

American (AMR) AF: 0.583 AC: 8894 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3472

East Asian (EAS) AF: 0.505 AC: 2597 AN: 5140

South Asian (SAS) AF: 0.608 AC: 2924 AN: 4806

European-Finnish (FIN) AF: 0.530 AC: 5568 AN: 10504

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35312 AN: 67914

Other (OTH) AF: 0.592 AC: 1250 AN: 2110

Alfa AF: 0.536 Hom.: 34447

Bravo AF: 0.602

Asia WGS AF: 0.629 AC: 2187 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.062
DANN	Benign	0.36
PhyloP100		-4.6

Splicing

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

Other links and lift over

dbSNP: rs2256573; hg19: chr10-81685062;