10-79931278-A-G

Variant names:

• chr10-79931278-A-G
• rs2758555
• ENST00000453174.7:n.743-448A>G

Variant summary

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

The ENST00000453174.7(ENSG00000283913):​n.743-448A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.677 in 152,120 control chromosomes in the GnomAD database, including 35,717 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 0.68 (35717 hom., cov: 32)
• Consequence: ENSG00000283913 ENST00000453174.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00900
• Publications: 4 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMS1P21	NR_033857.1		n.743-448A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283913	ENST00000453174.7	TSL:2	n.743-448A>G		intron	N/A
	ENSG00000283913	ENST00000818194.1		n.634-18750A>G		intron	N/A
	ENSG00000283913	ENST00000818195.1		n.829-448A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.677 AC: 102884 AN: 152002 Hom.: 35659 Cov.: 32

Gnomad AFR AF: 0.825

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.647

Gnomad ASJ AF: 0.638

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.734

Gnomad FIN AF: 0.590

Gnomad MID AF: 0.701

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.666

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

GnomAD4 genome AF: 0.677 AC: 103007 AN: 152120 Hom.: 35717 Cov.: 32 AF XY: 0.679 AC XY: 50473 AN XY: 74366

African (AFR) AF: 0.825 AC: 34259 AN: 41506

American (AMR) AF: 0.648 AC: 9905 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.638 AC: 2215 AN: 3470

East Asian (EAS) AF: 0.778 AC: 4030 AN: 5182

South Asian (SAS) AF: 0.735 AC: 3545 AN: 4824

European-Finnish (FIN) AF: 0.590 AC: 6238 AN: 10564

Middle Eastern (MID) AF: 0.695 AC: 203 AN: 292

European-Non Finnish (NFE) AF: 0.598 AC: 40632 AN: 67982

Other (OTH) AF: 0.670 AC: 1414 AN: 2110

Alfa AF: 0.622 Hom.: 128791

Bravo AF: 0.685

Asia WGS AF: 0.772 AC: 2685 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	11
DANN	Benign	0.85
PhyloP100		-0.0090

Splicing

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

Other links and lift over

dbSNP: rs2758555; hg19: chr10-81691034;