rs3802966

Variant names:

• chr11-18527416-G-C
• rs3802966
• ENST00000690266.2:n.460G>C

Variant summary

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

The ENST00000690266.2(ENSG00000289499):​n.460G>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.202 in 152,082 control chromosomes in the GnomAD database, including 3,256 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 0.20 (3256 hom., cov: 32)
• Consequence: ENSG00000289499 ENST00000690266.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.492
• Publications: 4 publications found

Genes affected

ENSG00000289499 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.244 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
ENSG00000289499	ENST00000690266.2	n.460G>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.202 AC: 30716 AN: 151964 Hom.: 3250 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.193

Gnomad AMR AF: 0.228

Gnomad ASJ AF: 0.233

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.225

Gnomad FIN AF: 0.140

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.180

Gnomad OTH AF: 0.203

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

GnomAD4 genome AF: 0.202 AC: 30733 AN: 152082 Hom.: 3256 Cov.: 32 AF XY: 0.199 AC XY: 14776 AN XY: 74346

African (AFR) AF: 0.233 AC: 9679 AN: 41462

American (AMR) AF: 0.228 AC: 3481 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.233 AC: 808 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1323 AN: 5180

South Asian (SAS) AF: 0.226 AC: 1089 AN: 4826

European-Finnish (FIN) AF: 0.140 AC: 1479 AN: 10564

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.179 AC: 12205 AN: 67996

Other (OTH) AF: 0.202 AC: 426 AN: 2110

Alfa AF: 0.191 Hom.: 356

Bravo AF: 0.212

Asia WGS AF: 0.220 AC: 766 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.3
DANN	Benign	0.54
PhyloP100		-0.49
PromoterAI		-0.038	Neutral

Splicing

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

Other links and lift over

dbSNP: rs3802966; hg19: chr11-18548963;