rs7893928

Variant names:

• chr10-44583495-C-T
• rs7893928
• ENST00000738582.1:n.90+540C>T

Variant summary

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

The ENST00000738582.1(ENSG00000296361):​n.90+540C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.131 in 151,872 control chromosomes in the GnomAD database, including 1,327 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 0.13 (1327 hom., cov: 31)
• Consequence: ENSG00000296361 ENST00000738582.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0360
• Publications: 4 publications found

Genes affected

ENSG00000296361 (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 (NFE) allele frequency at 95% confidence interval = 0.147 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000738582.1. 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
	ENSG00000296361	ENST00000738582.1		n.90+540C>T		intron	N/A
	ENSG00000296361	ENST00000738583.1		n.90+540C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.131 AC: 19944 AN: 151754 Hom.: 1329 Cov.: 31

Gnomad AFR AF: 0.134

Gnomad AMI AF: 0.0789

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.111

Gnomad EAS AF: 0.00155

Gnomad SAS AF: 0.0914

Gnomad FIN AF: 0.144

Gnomad MID AF: 0.146

Gnomad NFE AF: 0.149

Gnomad OTH AF: 0.129

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

GnomAD4 genome AF: 0.131 AC: 19939 AN: 151872 Hom.: 1327 Cov.: 31 AF XY: 0.129 AC XY: 9568 AN XY: 74204

African (AFR) AF: 0.134 AC: 5534 AN: 41360

American (AMR) AF: 0.100 AC: 1533 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.111 AC: 384 AN: 3470

East Asian (EAS) AF: 0.00155 AC: 8 AN: 5164

South Asian (SAS) AF: 0.0904 AC: 434 AN: 4800

European-Finnish (FIN) AF: 0.144 AC: 1515 AN: 10536

Middle Eastern (MID) AF: 0.147 AC: 43 AN: 292

European-Non Finnish (NFE) AF: 0.149 AC: 10147 AN: 67958

Other (OTH) AF: 0.128 AC: 269 AN: 2108

Alfa AF: 0.137 Hom.: 1238

Bravo AF: 0.126

Asia WGS AF: 0.0480 AC: 167 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	1.9
DANN	Benign	0.42
PhyloP100		-0.036

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7893928;

hg19: chr10-45078943;