ENST00000453174.7:n.742+3526G>A

Variant names:

• chr10-79925514-G-A
• rs7911085
• ENST00000453174.7:n.742+3526G>A

Variant summary

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

The ENST00000453174.7(ENSG00000283913):​n.742+3526G>A variant causes a intron 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: ENSG00000283913 ENST00000453174.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.318
• 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 = 0.35 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453174.7. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMS1P21	NR_033857.1		n.742+3526G>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283913	ENST00000453174.7	TSL:2	n.742+3526G>A		intron	N/A
	ENSG00000283913	ENST00000818194.1		n.633+17658G>A		intron	N/A
	ENSG00000283913	ENST00000818195.1		n.829-6212G>A		intron	N/A

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

African (AFR) AF: 0.354 AC: 14688 AN: 41442

American (AMR) AF: 0.133 AC: 2029 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0844 AC: 293 AN: 3472

East Asian (EAS) AF: 0.274 AC: 1421 AN: 5178

South Asian (SAS) AF: 0.139 AC: 670 AN: 4814

European-Finnish (FIN) AF: 0.163 AC: 1724 AN: 10582

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.140 AC: 9527 AN: 67998

Other (OTH) AF: 0.185 AC: 392 AN: 2114

Alfa AF: 0.157 Hom.: 9573

Bravo AF: 0.212

Asia WGS AF: 0.170 AC: 593 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.79
DANN	Benign	0.20
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs7911085; hg19: chr10-81685270;