rs11597219

Positions:

• chr10-79927885-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_033857.1(BMS1P21):​n.743-3841C>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 0.0155 in 152,280 control chromosomes in the GnomAD database, including 31 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 0.015 (31 hom., cov: 32)
• Consequence: BMS1P21 NR_033857.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197

Genes affected

BMS1P21 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0155 (2358/152280) while in subpopulation NFE AF= 0.0236 (1604/68020). AF 95% confidence interval is 0.0226. There are 31 homozygotes in gnomad4. There are 1127 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd4 at 31 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BMS1P21	NR_033857.1	n.743-3841C>T		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.0155 AC: 2358 AN: 152162 Hom.: 31 Cov.: 32

Gnomad AFR AF: 0.00396

Gnomad AMI AF: 0.00879

Gnomad AMR AF: 0.0126

Gnomad ASJ AF: 0.0337

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00186

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.00633

Gnomad NFE AF: 0.0236

Gnomad OTH AF: 0.0129

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

GnomAD4 genome AF: 0.0155 AC: 2358 AN: 152280 Hom.: 31 Cov.: 32 AF XY: 0.0151 AC XY: 1127 AN XY: 74454

Gnomad4 AFR AF: 0.00395

Gnomad4 AMR AF: 0.0126

Gnomad4 ASJ AF: 0.0337

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.00186

Gnomad4 FIN AF: 0.0220

Gnomad4 NFE AF: 0.0236

Gnomad4 OTH AF: 0.0128

Alfa AF: 0.0197 Hom.: 12

Bravo AF: 0.0139

Asia WGS AF: 0.00375 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.41

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11597219; hg19: chr10-81687641;