rs10264084

Variant names:

• chr7-150895274-A-T
• rs10264084
• ENST00000726373.1:n.221+6121T>A

Variant summary

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

The ENST00000726373.1(ENSG00000289052):​n.221+6121T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,172 control chromosomes in the GnomAD database, including 2,583 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 0.18 (2583 hom., cov: 32)
• Consequence: ENSG00000289052 ENST00000726373.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.493
• Publications: 2 publications found

Genes affected

ENSG00000289052 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.244 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000726373.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289052	ENST00000726373.1		n.221+6121T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26649 AN: 152054 Hom.: 2576 Cov.: 32

Gnomad AFR AF: 0.248

Gnomad AMI AF: 0.188

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.145

Gnomad EAS AF: 0.0541

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.175 AC: 26678 AN: 152172 Hom.: 2583 Cov.: 32 AF XY: 0.171 AC XY: 12689 AN XY: 74406

African (AFR) AF: 0.248 AC: 10297 AN: 41484

American (AMR) AF: 0.131 AC: 2003 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.145 AC: 503 AN: 3470

East Asian (EAS) AF: 0.0544 AC: 282 AN: 5184

South Asian (SAS) AF: 0.150 AC: 723 AN: 4832

European-Finnish (FIN) AF: 0.134 AC: 1422 AN: 10602

Middle Eastern (MID) AF: 0.177 AC: 52 AN: 294

European-Non Finnish (NFE) AF: 0.160 AC: 10855 AN: 68004

Other (OTH) AF: 0.175 AC: 370 AN: 2112

Alfa AF: 0.175 Hom.: 291

Bravo AF: 0.177

Asia WGS AF: 0.119 AC: 414 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.4
DANN	Benign	0.43
PhyloP100		-0.49

Splicing

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

Other links and lift over

dbSNP: rs10264084; hg19: chr7-150592362;