18-3328781-A-G

Variant names:

• chr18-3328781-A-G
• rs1613695
• ENST00000578787.3:n.1202+1343A>G

Variant summary

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

The ENST00000578787.3(ENSG00000266578):​n.1202+1343A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.971 in 152,322 control chromosomes in the GnomAD database, including 71,889 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 0.97 (71889 hom., cov: 33)
• Consequence: ENSG00000266578 ENST00000578787.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.502
• Publications: 2 publications found

Genes affected

ENSG00000266578 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.985 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
ENSG00000266578	ENST00000578787.3	n.1202+1343A>G		intron_variant	Intron 2 of 2	3
ENSG00000301728	ENST00000781104.1	n.61+1845T>C		intron_variant	Intron 1 of 2
ENSG00000301728	ENST00000781105.1	n.114+1845T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.971 AC: 147841 AN: 152204 Hom.: 71838 Cov.: 33

Gnomad AFR AF: 0.993

Gnomad AMI AF: 0.975

Gnomad AMR AF: 0.930

Gnomad ASJ AF: 0.977

Gnomad EAS AF: 0.999

Gnomad SAS AF: 0.979

Gnomad FIN AF: 0.946

Gnomad MID AF: 0.994

Gnomad NFE AF: 0.968

Gnomad OTH AF: 0.978

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

GnomAD4 genome AF: 0.971 AC: 147951 AN: 152322 Hom.: 71889 Cov.: 33 AF XY: 0.970 AC XY: 72213 AN XY: 74484

African (AFR) AF: 0.993 AC: 41303 AN: 41580

American (AMR) AF: 0.930 AC: 14216 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.977 AC: 3391 AN: 3470

East Asian (EAS) AF: 0.999 AC: 5180 AN: 5184

South Asian (SAS) AF: 0.978 AC: 4722 AN: 4828

European-Finnish (FIN) AF: 0.946 AC: 10041 AN: 10618

Middle Eastern (MID) AF: 0.993 AC: 292 AN: 294

European-Non Finnish (NFE) AF: 0.968 AC: 65853 AN: 68038

Other (OTH) AF: 0.978 AC: 2064 AN: 2110

Alfa AF: 0.970 Hom.: 13970

Bravo AF: 0.972

Asia WGS AF: 0.989 AC: 3439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	15
DANN	Benign	0.58
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs1613695; hg19: chr18-3328779;