rs2052011

Variant names:

• chr17-13396246-C-G
• rs2052011
• ENST00000767988.1:n.204-9057G>C

Variant summary

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

The ENST00000767988.1(ENSG00000300019):​n.204-9057G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.903 in 152,316 control chromosomes in the GnomAD database, including 62,335 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 0.90 (62335 hom., cov: 35)
• Consequence: ENSG00000300019 ENST00000767988.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.04
• Publications: 1 publications found

Genes affected

ENSG00000300019 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300019	ENST00000767988.1	n.204-9057G>C		intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes AF: 0.903 AC: 137438 AN: 152198 Hom.: 62298 Cov.: 35

Gnomad AFR AF: 0.827

Gnomad AMI AF: 0.865

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.940

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.928

Gnomad FIN AF: 0.914

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.928

Gnomad OTH AF: 0.905

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

GnomAD4 genome AF: 0.903 AC: 137530 AN: 152316 Hom.: 62335 Cov.: 35 AF XY: 0.904 AC XY: 67347 AN XY: 74478

African (AFR) AF: 0.827 AC: 34378 AN: 41562

American (AMR) AF: 0.943 AC: 14424 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.940 AC: 3263 AN: 3472

East Asian (EAS) AF: 0.996 AC: 5145 AN: 5164

South Asian (SAS) AF: 0.927 AC: 4481 AN: 4832

European-Finnish (FIN) AF: 0.914 AC: 9710 AN: 10622

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.928 AC: 63154 AN: 68040

Other (OTH) AF: 0.906 AC: 1918 AN: 2116

Alfa AF: 0.919 Hom.: 8001

Bravo AF: 0.904

Asia WGS AF: 0.952 AC: 3310 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.057
DANN	Benign	0.42
PhyloP100		-1.0

Splicing

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

Other links and lift over

dbSNP: rs2052011; hg19: chr17-13299563;