chr7-15066869-G-C

Variant names:

• chr7-15066869-G-C
• rs11772451
• ENST00000445093.1:n.306+357G>C

Variant summary

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

The ENST00000445093.1(ENSG00000227489):​n.306+357G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.39 in 151,728 control chromosomes in the GnomAD database, including 14,816 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 0.39 (14816 hom., cov: 32)
• Consequence: ENSG00000227489 ENST00000445093.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.12
• Publications: 3 publications found

Genes affected

ENSG00000227489 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.688 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445093.1. 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
	ENSG00000227489	ENST00000445093.1	TSL:3	n.306+357G>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.390 AC: 59123 AN: 151610 Hom.: 14771 Cov.: 32

Gnomad AFR AF: 0.694

Gnomad AMI AF: 0.157

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.558

Gnomad SAS AF: 0.258

Gnomad FIN AF: 0.304

Gnomad MID AF: 0.263

Gnomad NFE AF: 0.233

Gnomad OTH AF: 0.334

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

GnomAD4 genome AF: 0.390 AC: 59218 AN: 151728 Hom.: 14816 Cov.: 32 AF XY: 0.394 AC XY: 29182 AN XY: 74160

African (AFR) AF: 0.695 AC: 28766 AN: 41400

American (AMR) AF: 0.380 AC: 5791 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 606 AN: 3462

East Asian (EAS) AF: 0.558 AC: 2867 AN: 5142

South Asian (SAS) AF: 0.257 AC: 1234 AN: 4798

European-Finnish (FIN) AF: 0.304 AC: 3201 AN: 10540

Middle Eastern (MID) AF: 0.259 AC: 76 AN: 294

European-Non Finnish (NFE) AF: 0.233 AC: 15831 AN: 67860

Other (OTH) AF: 0.335 AC: 704 AN: 2102

Alfa AF: 0.173 Hom.: 381

Bravo AF: 0.413

Asia WGS AF: 0.429 AC: 1486 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.23
DANN	Benign	0.38
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11772451; hg19: chr7-15106494;