17-49999071-A-G

Variant names:

• chr17-49999071-A-G
• rs11079884
• ENST00000511867.1:n.139+2044A>G

Variant summary

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

The ENST00000511867.1(ENSG00000248172):​n.139+2044A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.127 in 152,110 control chromosomes in the GnomAD database, including 1,289 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 (1289 hom., cov: 32)
• Consequence: ENSG00000248172 ENST00000511867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0780
• Publications: 8 publications found

Genes affected

ENSG00000248172 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.135 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511867.1. 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
	ENSG00000248172	ENST00000511867.1	TSL:2	n.139+2044A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.127 AC: 19340 AN: 151992 Hom.: 1287 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.155

Gnomad AMR AF: 0.0987

Gnomad ASJ AF: 0.173

Gnomad EAS AF: 0.0990

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.175

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.137

Gnomad OTH AF: 0.119

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

GnomAD4 genome AF: 0.127 AC: 19358 AN: 152110 Hom.: 1289 Cov.: 32 AF XY: 0.128 AC XY: 9541 AN XY: 74350

African (AFR) AF: 0.109 AC: 4537 AN: 41492

American (AMR) AF: 0.0985 AC: 1506 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.173 AC: 599 AN: 3470

East Asian (EAS) AF: 0.0989 AC: 510 AN: 5158

South Asian (SAS) AF: 0.125 AC: 602 AN: 4814

European-Finnish (FIN) AF: 0.175 AC: 1858 AN: 10588

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.137 AC: 9318 AN: 67990

Other (OTH) AF: 0.118 AC: 249 AN: 2108

Alfa AF: 0.132 Hom.: 2351

Bravo AF: 0.119

Asia WGS AF: 0.108 AC: 378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	4.7
DANN	Benign	0.55
PhyloP100		0.078

Splicing

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

Other links and lift over

dbSNP: rs11079884; hg19: chr17-48076435;