17-49980509-G-A

Variant names:

• chr17-49980509-G-A
• rs11079881
• ENST00000771344.1:n.411+33C>T

Variant summary

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

The ENST00000771344.1(ENSG00000300397):​n.411+33C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.779 in 152,090 control chromosomes in the GnomAD database, including 48,622 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 0.78 (48622 hom., cov: 32)
• Consequence: ENSG00000300397 ENST00000771344.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0750
• Publications: 3 publications found

Genes affected

ENSG00000300397 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.949 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000771344.1. 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
	ENSG00000300397	ENST00000771344.1		n.411+33C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.779 AC: 118420 AN: 151972 Hom.: 48615 Cov.: 32

Gnomad AFR AF: 0.490

Gnomad AMI AF: 0.891

Gnomad AMR AF: 0.864

Gnomad ASJ AF: 0.921

Gnomad EAS AF: 0.971

Gnomad SAS AF: 0.801

Gnomad FIN AF: 0.894

Gnomad MID AF: 0.759

Gnomad NFE AF: 0.892

Gnomad OTH AF: 0.802

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

GnomAD4 genome AF: 0.779 AC: 118463 AN: 152090 Hom.: 48622 Cov.: 32 AF XY: 0.781 AC XY: 58054 AN XY: 74338

African (AFR) AF: 0.490 AC: 20276 AN: 41414

American (AMR) AF: 0.864 AC: 13211 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.921 AC: 3194 AN: 3468

East Asian (EAS) AF: 0.971 AC: 5018 AN: 5166

South Asian (SAS) AF: 0.803 AC: 3867 AN: 4816

European-Finnish (FIN) AF: 0.894 AC: 9479 AN: 10600

Middle Eastern (MID) AF: 0.779 AC: 229 AN: 294

European-Non Finnish (NFE) AF: 0.892 AC: 60683 AN: 68014

Other (OTH) AF: 0.802 AC: 1693 AN: 2112

Alfa AF: 0.868 Hom.: 137320

Bravo AF: 0.767

Asia WGS AF: 0.842 AC: 2926 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.5
DANN	Benign	0.70
PhyloP100		0.075

Splicing

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

Other links and lift over

dbSNP: rs11079881; hg19: chr17-48057873;