chr11-87493416-G-A

Variant names:

• chr11-87493416-G-A
• rs7925637
• ENST00000784851.1:n.476-59883G>A

Variant summary

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

The ENST00000784851.1(ENSG00000302190):​n.476-59883G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.279 in 151,914 control chromosomes in the GnomAD database, including 6,848 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 0.28 (6848 hom., cov: 32)
• Consequence: ENSG00000302190 ENST00000784851.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0650
• Publications: 2 publications found

Genes affected

ENSG00000302190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000784851.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302190	ENST00000784851.1		n.476-59883G>A		intron	N/A
	ENSG00000302190	ENST00000784852.1		n.179+39027G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.279 AC: 42365 AN: 151796 Hom.: 6829 Cov.: 32

Gnomad AFR AF: 0.452

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.208

Gnomad ASJ AF: 0.159

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.241

Gnomad FIN AF: 0.243

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.240

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

GnomAD4 genome AF: 0.279 AC: 42423 AN: 151914 Hom.: 6848 Cov.: 32 AF XY: 0.280 AC XY: 20822 AN XY: 74264

African (AFR) AF: 0.452 AC: 18699 AN: 41370

American (AMR) AF: 0.208 AC: 3174 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.159 AC: 551 AN: 3468

East Asian (EAS) AF: 0.260 AC: 1344 AN: 5166

South Asian (SAS) AF: 0.240 AC: 1159 AN: 4822

European-Finnish (FIN) AF: 0.243 AC: 2559 AN: 10544

Middle Eastern (MID) AF: 0.265 AC: 78 AN: 294

European-Non Finnish (NFE) AF: 0.209 AC: 14212 AN: 67960

Other (OTH) AF: 0.239 AC: 505 AN: 2110

Alfa AF: 0.223 Hom.: 2134

Bravo AF: 0.282

Asia WGS AF: 0.275 AC: 957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.0
DANN	Benign	0.33
PhyloP100		0.065

Splicing

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

Other links and lift over

dbSNP: rs7925637; hg19: chr11-87204458;