10-79926324-C-T

Variant names:

• chr10-79926324-C-T
• rs2819106
• ENST00000453174.7:n.742+4336C>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+4336C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.681 in 152,114 control chromosomes in the GnomAD database, including 36,212 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 0.68 (36212 hom., cov: 32)
• Consequence: ENSG00000283913 ENST00000453174.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• Publications: 2 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=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.83 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
BMS1P21	NR_033857.1	n.742+4336C>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+4336C>T		intron_variant	Intron 5 of 7	2
ENSG00000283913	ENST00000818194.1	n.633+18468C>T		intron_variant	Intron 3 of 3
ENSG00000283913	ENST00000818195.1	n.829-5402C>T		intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes AF: 0.681 AC: 103519 AN: 151996 Hom.: 36148 Cov.: 32

Gnomad AFR AF: 0.837

Gnomad AMI AF: 0.624

Gnomad AMR AF: 0.650

Gnomad ASJ AF: 0.639

Gnomad EAS AF: 0.777

Gnomad SAS AF: 0.740

Gnomad FIN AF: 0.593

Gnomad MID AF: 0.699

Gnomad NFE AF: 0.598

Gnomad OTH AF: 0.672

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

GnomAD4 genome AF: 0.681 AC: 103650 AN: 152114 Hom.: 36212 Cov.: 32 AF XY: 0.683 AC XY: 50805 AN XY: 74360

African (AFR) AF: 0.837 AC: 34760 AN: 41524

American (AMR) AF: 0.651 AC: 9958 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.639 AC: 2219 AN: 3470

East Asian (EAS) AF: 0.777 AC: 4015 AN: 5168

South Asian (SAS) AF: 0.741 AC: 3562 AN: 4808

European-Finnish (FIN) AF: 0.593 AC: 6264 AN: 10572

Middle Eastern (MID) AF: 0.694 AC: 204 AN: 294

European-Non Finnish (NFE) AF: 0.598 AC: 40673 AN: 67962

Other (OTH) AF: 0.676 AC: 1426 AN: 2108

Alfa AF: 0.624 Hom.: 15194

Bravo AF: 0.689

Asia WGS AF: 0.773 AC: 2690 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	5.4
DANN	Benign	0.45
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs2819106; hg19: chr10-81686080;