chr10-79927885-C-T

Variant names:

• chr10-79927885-C-T
• rs11597219
• ENST00000453174.7:n.743-3841C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000453174.7(ENSG00000283913):​n.743-3841C>T variant causes a intron 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: ENSG00000283913 ENST00000453174.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.197
• Publications: 1 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=-0.86).
• 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 the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 31 gene

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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	BMS1P21	NR_033857.1		n.743-3841C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000283913	ENST00000453174.7	TSL:2	n.743-3841C>T		intron	N/A
	ENSG00000283913	ENST00000818194.1		n.633+20029C>T		intron	N/A
	ENSG00000283913	ENST00000818195.1		n.829-3841C>T		intron	N/A

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

African (AFR) AF: 0.00395 AC: 164 AN: 41554

American (AMR) AF: 0.0126 AC: 193 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0337 AC: 117 AN: 3470

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00186 AC: 9 AN: 4828

European-Finnish (FIN) AF: 0.0220 AC: 233 AN: 10608

Middle Eastern (MID) AF: 0.00680 AC: 2 AN: 294

European-Non Finnish (NFE) AF: 0.0236 AC: 1604 AN: 68020

Other (OTH) AF: 0.0128 AC: 27 AN: 2112

Alfa AF: 0.0200 Hom.: 13

Bravo AF: 0.0139

Asia WGS AF: 0.00375 AC: 15 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.5
DANN	Benign	0.41
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs11597219; hg19: chr10-81687641;