rs1595963

Variant names:

• chr18-29880383-G-C
• rs1595963
• ENST00000803180.1:n.164+41281C>G

Variant summary

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

The ENST00000803180.1(ENSG00000304402):​n.164+41281C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.041 in 152,134 control chromosomes in the GnomAD database, including 189 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 0.041 (189 hom., cov: 32)
• Consequence: ENSG00000304402 ENST00000803180.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.252
• Publications: 1 publications found

Genes affected

ENSG00000304402 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0837 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
ENSG00000304402	ENST00000803180.1	n.164+41281C>G		intron_variant	Intron 1 of 2
ENSG00000304402	ENST00000803181.1	n.164+41281C>G		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0410 AC: 6228 AN: 152016 Hom.: 187 Cov.: 32

Gnomad AFR AF: 0.0695

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.0462

Gnomad ASJ AF: 0.0181

Gnomad EAS AF: 0.0903

Gnomad SAS AF: 0.0315

Gnomad FIN AF: 0.0174

Gnomad MID AF: 0.0348

Gnomad NFE AF: 0.0248

Gnomad OTH AF: 0.0363

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

GnomAD4 genome AF: 0.0410 AC: 6240 AN: 152134 Hom.: 189 Cov.: 32 AF XY: 0.0406 AC XY: 3018 AN XY: 74350

African (AFR) AF: 0.0695 AC: 2881 AN: 41458

American (AMR) AF: 0.0462 AC: 707 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0181 AC: 63 AN: 3472

East Asian (EAS) AF: 0.0905 AC: 467 AN: 5160

South Asian (SAS) AF: 0.0311 AC: 150 AN: 4820

European-Finnish (FIN) AF: 0.0174 AC: 184 AN: 10592

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0248 AC: 1687 AN: 68018

Other (OTH) AF: 0.0378 AC: 80 AN: 2114

Alfa AF: 0.0314 Hom.: 22

Bravo AF: 0.0462

Asia WGS AF: 0.0720 AC: 252 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.2
DANN	Benign	0.52
PhyloP100		0.25

Splicing

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

Other links and lift over

dbSNP: rs1595963; hg19: chr18-27460348;