chr10-79924588-C-T

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000283913 (HGNC:):

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMS1P21	NR_033857.1	n.742+2600C>T		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283913	ENST00000453174.7	n.742+2600C>T		intron_variant	Intron 5 of 7	2

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

Gnomad4 AFR AF: 0.0969

Gnomad4 AMR AF: 0.183

Gnomad4 ASJ AF: 0.233

Gnomad4 EAS AF: 0.482

Gnomad4 SAS AF: 0.347

Gnomad4 FIN AF: 0.300

Gnomad4 NFE AF: 0.272

Gnomad4 OTH AF: 0.212

Alfa AF: 0.226 Hom.: 842

Bravo AF: 0.207

Asia WGS AF: 0.403 AC: 1401 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.44

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2256703; hg19: chr10-81684344;