chr17-41001135-G-A

Variant names:

• chr17-41001135-G-A
• rs7224319
• ENST00000815517.1:n.219+20528G>A

Variant summary

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

The ENST00000815517.1(ENSG00000306126):​n.219+20528G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,122 control chromosomes in the GnomAD database, including 6,929 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 0.23 (6929 hom., cov: 33)
• Consequence: ENSG00000306126 ENST00000815517.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.588
• Publications: 2 publications found

Genes affected

ENSG00000306126 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.528 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000815517.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306126	ENST00000815517.1		n.219+20528G>A		intron	N/A
	ENSG00000306126	ENST00000815518.1		n.159+20528G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35412 AN: 152004 Hom.: 6896 Cov.: 33

Gnomad AFR AF: 0.533

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.0775

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.120

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.0898

Gnomad OTH AF: 0.205

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

GnomAD4 genome AF: 0.233 AC: 35490 AN: 152122 Hom.: 6929 Cov.: 33 AF XY: 0.234 AC XY: 17378 AN XY: 74362

African (AFR) AF: 0.534 AC: 22142 AN: 41450

American (AMR) AF: 0.205 AC: 3128 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0775 AC: 269 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1259 AN: 5180

South Asian (SAS) AF: 0.168 AC: 809 AN: 4816

European-Finnish (FIN) AF: 0.120 AC: 1270 AN: 10580

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.0898 AC: 6106 AN: 68012

Other (OTH) AF: 0.203 AC: 429 AN: 2114

Alfa AF: 0.154 Hom.: 489

Bravo AF: 0.256

Asia WGS AF: 0.238 AC: 828 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.53
DANN	Benign	0.71
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs7224319; hg19: chr17-39157387;