rs2017620

Variant names:

• chr7-5796087-A-G
• rs2017620
• ENST00000803091.1:n.423+1200A>G

Variant summary

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

The ENST00000803091.1(ENSG00000304383):​n.423+1200A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.353 in 151,836 control chromosomes in the GnomAD database, including 10,903 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 0.35 (10903 hom., cov: 31)
• Consequence: ENSG00000304383 ENST00000803091.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.25
• Publications: 0 publications found

Genes affected

ENSG00000304383 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.725 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
ENSG00000304383	ENST00000803091.1	n.423+1200A>G		intron_variant	Intron 1 of 1
ENSG00000304383	ENST00000803092.1	n.417+1200A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.354 AC: 53649 AN: 151718 Hom.: 10904 Cov.: 31

Gnomad AFR AF: 0.166

Gnomad AMI AF: 0.426

Gnomad AMR AF: 0.343

Gnomad ASJ AF: 0.550

Gnomad EAS AF: 0.745

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.430

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.411

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.353 AC: 53645 AN: 151836 Hom.: 10903 Cov.: 31 AF XY: 0.356 AC XY: 26410 AN XY: 74172

African (AFR) AF: 0.165 AC: 6857 AN: 41476

American (AMR) AF: 0.343 AC: 5217 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.550 AC: 1906 AN: 3468

East Asian (EAS) AF: 0.745 AC: 3840 AN: 5156

South Asian (SAS) AF: 0.421 AC: 2025 AN: 4812

European-Finnish (FIN) AF: 0.430 AC: 4521 AN: 10504

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.411 AC: 27891 AN: 67902

Other (OTH) AF: 0.408 AC: 860 AN: 2110

Alfa AF: 0.399 Hom.: 6506

Bravo AF: 0.342

Asia WGS AF: 0.499 AC: 1735 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.55
PhyloP100		-2.3

Splicing

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

Other links and lift over

dbSNP: rs2017620; hg19: chr7-5835718;