rs1923541

Variant names:

• chr10-79930539-C-A
• rs1923541
• ENST00000453174.7:n.743-1187C>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

The ENST00000453174.7(ENSG00000283913):​n.743-1187C>A variant causes a intron 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: ENSG00000283913 ENST00000453174.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.435
• Publications: 6 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=-0.83).
• 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 rank	MANE	Protein	UniProt
BMS1P21	NR_033857.1	n.743-1187C>A		intron_variant	Intron 5 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000283913	ENST00000453174.7	n.743-1187C>A		intron_variant	Intron 5 of 7	2
ENSG00000283913	ENST00000818194.1	n.634-19489C>A		intron_variant	Intron 3 of 3
ENSG00000283913	ENST00000818195.1	n.829-1187C>A		intron_variant	Intron 3 of 5
ENSG00000283913	ENST00000818196.1	n.394-1187C>A		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.697 AC: 28891 AN: 41476

American (AMR) AF: 0.446 AC: 6820 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.523 AC: 1814 AN: 3470

East Asian (EAS) AF: 0.761 AC: 3938 AN: 5174

South Asian (SAS) AF: 0.528 AC: 2544 AN: 4818

European-Finnish (FIN) AF: 0.537 AC: 5682 AN: 10574

Middle Eastern (MID) AF: 0.578 AC: 170 AN: 294

European-Non Finnish (NFE) AF: 0.509 AC: 34583 AN: 67968

Other (OTH) AF: 0.537 AC: 1133 AN: 2108

Alfa AF: 0.524 Hom.: 67530

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
PhyloP100		0.43

Splicing

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

Other links and lift over

dbSNP: rs1923541; hg19: chr10-81690295;