10-79924588-C-T

Variant names:

• chr10-79924588-C-T
• rs2256703
• ENST00000453174.7:n.742+2600C>T

Variant summary

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

The ENST00000453174.7(ENSG00000283913):​n.742+2600C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.225 in 152,162 control chromosomes in the GnomAD database, including 4,567 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 0.22 (4567 hom., cov: 33)
• Consequence: ENSG00000283913 ENST00000453174.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409
• Publications: 5 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=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.466 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+2600C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283913	ENST00000453174.7	TSL:2	n.742+2600C>T		intron	N/A
	ENSG00000283913	ENST00000818194.1		n.633+16732C>T		intron	N/A
	ENSG00000283913	ENST00000818195.1		n.829-7138C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.225 AC: 34153 AN: 152044 Hom.: 4564 Cov.: 33

Gnomad AFR AF: 0.0967

Gnomad AMI AF: 0.216

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.482

Gnomad SAS AF: 0.347

Gnomad FIN AF: 0.300

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.272

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.225 AC: 34179 AN: 152162 Hom.: 4567 Cov.: 33 AF XY: 0.229 AC XY: 17045 AN XY: 74388

African (AFR) AF: 0.0969 AC: 4023 AN: 41530

American (AMR) AF: 0.183 AC: 2806 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 809 AN: 3470

East Asian (EAS) AF: 0.482 AC: 2489 AN: 5168

South Asian (SAS) AF: 0.347 AC: 1670 AN: 4814

European-Finnish (FIN) AF: 0.300 AC: 3170 AN: 10584

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.272 AC: 18500 AN: 67980

Other (OTH) AF: 0.212 AC: 448 AN: 2114

Alfa AF: 0.223 Hom.: 845

Bravo AF: 0.207

Asia WGS AF: 0.403 AC: 1401 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	0.90
DANN	Benign	0.44
PhyloP100		-0.41

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2256703;

hg19: chr10-81684344;