rs1923541

Positions:

• chr10-79930539-C-A
• chr10-79930539-C-G

Variant summary

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

The NR_033857.1(BMS1P21):​n.743-1187C>A 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 0.566 in 152,086 control chromosomes in the GnomAD database, including 25,260 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 0.57 (25260 hom., cov: 33)
• Consequence: BMS1P21 NR_033857.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435

Genes affected

BMS1P21 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.741 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMS1P21	NR_033857.1	n.743-1187C>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.566 AC: 86055 AN: 151968 Hom.: 25237 Cov.: 33

Gnomad AFR AF: 0.697

Gnomad AMI AF: 0.612

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.523

Gnomad EAS AF: 0.761

Gnomad SAS AF: 0.527

Gnomad FIN AF: 0.537

Gnomad MID AF: 0.582

Gnomad NFE AF: 0.509

Gnomad OTH AF: 0.536

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

GnomAD4 genome AF: 0.566 AC: 86132 AN: 152086 Hom.: 25260 Cov.: 33 AF XY: 0.566 AC XY: 42071 AN XY: 74340

Gnomad4 AFR AF: 0.697

Gnomad4 AMR AF: 0.446

Gnomad4 ASJ AF: 0.523

Gnomad4 EAS AF: 0.761

Gnomad4 SAS AF: 0.528

Gnomad4 FIN AF: 0.537

Gnomad4 NFE AF: 0.509

Gnomad4 OTH AF: 0.537

Alfa AF: 0.515 Hom.: 41324

Bravo AF: 0.565

Asia WGS AF: 0.632 AC: 2201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.2
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1923541; hg19: chr10-81690295;