chr10-79925514-G-A

Position:

• chr10-79925514-G-A

Variant summary

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

The NR_033857.1(BMS1P21):​n.742+3526G>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 0.204 in 152,094 control chromosomes in the GnomAD database, including 3,991 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 0.20 (3991 hom., cov: 32)
• Consequence: BMS1P21 NR_033857.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318

Genes affected

BMS1P21 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.35 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BMS1P21	NR_033857.1	n.742+3526G>A		intron_variant, non_coding_transcript_variant

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.204 AC: 31069 AN: 151976 Hom.: 3994 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.318

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.0844

Gnomad EAS AF: 0.274

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.163

Gnomad MID AF: 0.171

Gnomad NFE AF: 0.140

Gnomad OTH AF: 0.185

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

GnomAD4 genome AF: 0.204 AC: 31081 AN: 152094 Hom.: 3991 Cov.: 32 AF XY: 0.203 AC XY: 15073 AN XY: 74340

Gnomad4 AFR AF: 0.354

Gnomad4 AMR AF: 0.133

Gnomad4 ASJ AF: 0.0844

Gnomad4 EAS AF: 0.274

Gnomad4 SAS AF: 0.139

Gnomad4 FIN AF: 0.163

Gnomad4 NFE AF: 0.140

Gnomad4 OTH AF: 0.185

Alfa AF: 0.146 Hom.: 3776

Bravo AF: 0.212

Asia WGS AF: 0.170 AC: 593 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	0.79
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7911085; hg19: chr10-81685270;