rs9966412

Variant names:

• chr18-60366702-C-T
• rs9966412
• ENST00000650201.1:n.113+37357C>T

Variant summary

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

The ENST00000650201.1(ENSG00000285681):​n.113+37357C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.244 in 152,016 control chromosomes in the GnomAD database, including 7,584 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 0.24 (7584 hom., cov: 32)
• Consequence: ENSG00000285681 ENST00000650201.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.177
• Publications: 10 publications found

Genes affected

ENSG00000285681 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.555 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
ENSG00000285681	ENST00000650201.1	n.113+37357C>T		intron_variant	Intron 1 of 3
ENSG00000285681	ENST00000658928.1	n.156+37357C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.244 AC: 37051 AN: 151898 Hom.: 7550 Cov.: 32

Gnomad AFR AF: 0.560

Gnomad AMI AF: 0.104

Gnomad AMR AF: 0.185

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.0932

Gnomad SAS AF: 0.122

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.139

Gnomad NFE AF: 0.116

Gnomad OTH AF: 0.211

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

GnomAD4 genome AF: 0.244 AC: 37130 AN: 152016 Hom.: 7584 Cov.: 32 AF XY: 0.239 AC XY: 17784 AN XY: 74306

African (AFR) AF: 0.561 AC: 23244 AN: 41434

American (AMR) AF: 0.185 AC: 2824 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.121 AC: 419 AN: 3468

East Asian (EAS) AF: 0.0931 AC: 481 AN: 5168

South Asian (SAS) AF: 0.120 AC: 575 AN: 4808

European-Finnish (FIN) AF: 0.104 AC: 1097 AN: 10558

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.116 AC: 7907 AN: 67968

Other (OTH) AF: 0.210 AC: 445 AN: 2116

Alfa AF: 0.210 Hom.: 1294

Bravo AF: 0.268

Asia WGS AF: 0.153 AC: 532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.79
DANN	Benign	0.19
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs9966412; hg19: chr18-58033935;