10-79924588-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NR_033857.1(BMS1P21):n.742+2600C>T variant causes a intron, non coding transcript 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: BMS1P21 NR_033857.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.409

Genes affected

BMS1P21 (HGNC:):

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/exons	MANE	UniProt
BMS1P21	NR_033857.1	n.742+2600C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

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;