chr10-79925039-G-A

Variant names:

• chr10-79925039-G-A
• rs2256588
• ENST00000453174.7:n.742+3051G>A

Variant summary

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

The ENST00000453174.7(ENSG00000283913):​n.742+3051G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.598 in 151,960 control chromosomes in the GnomAD database, including 28,032 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 0.60 (28032 hom., cov: 32)
• Consequence: ENSG00000283913 ENST00000453174.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.262
• Publications: 2 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=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.757 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+3051G>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283913	ENST00000453174.7	TSL:2	n.742+3051G>A		intron	N/A
	ENSG00000283913	ENST00000818194.1		n.633+17183G>A		intron	N/A
	ENSG00000283913	ENST00000818195.1		n.829-6687G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.597 AC: 90670 AN: 151842 Hom.: 27975 Cov.: 32

Gnomad AFR AF: 0.763

Gnomad AMI AF: 0.558

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.553

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.617

Gnomad FIN AF: 0.516

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.520

Gnomad OTH AF: 0.592

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

GnomAD4 genome AF: 0.598 AC: 90797 AN: 151960 Hom.: 28032 Cov.: 32 AF XY: 0.597 AC XY: 44321 AN XY: 74290

African (AFR) AF: 0.764 AC: 31665 AN: 41450

American (AMR) AF: 0.585 AC: 8945 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.553 AC: 1919 AN: 3470

East Asian (EAS) AF: 0.503 AC: 2591 AN: 5150

South Asian (SAS) AF: 0.616 AC: 2961 AN: 4806

European-Finnish (FIN) AF: 0.516 AC: 5444 AN: 10548

Middle Eastern (MID) AF: 0.588 AC: 173 AN: 294

European-Non Finnish (NFE) AF: 0.520 AC: 35341 AN: 67950

Other (OTH) AF: 0.594 AC: 1254 AN: 2110

Alfa AF: 0.566 Hom.: 3089

Bravo AF: 0.607

Asia WGS AF: 0.631 AC: 2193 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.64
DANN	Benign	0.40
PhyloP100		-0.26

Splicing

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

Other links and lift over

dbSNP: rs2256588; hg19: chr10-81684795;