rs35996865

Variant names:

• chr18-21112383-T-G
• rs35996865
• ENST00000833849.1:n.513T>G

Variant summary

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

The ENST00000833849.1(ENSG00000308413):​n.513T>G 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 0.279 in 152,162 control chromosomes in the GnomAD database, including 6,831 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 0.28 (6831 hom., cov: 33)
• Consequence: ENSG00000308413 ENST00000833849.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360
• Publications: 21 publications found

Genes affected

ENSG00000308413 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.76).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.435 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
ENSG00000308413	ENST00000833849.1	n.513T>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000308413	ENST00000833850.1	n.440T>G		non_coding_transcript_exon_variant	Exon 1 of 3
ENSG00000308413	ENST00000833851.1	n.196T>G		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42306 AN: 152042 Hom.: 6814 Cov.: 33

Gnomad AFR AF: 0.440

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.327

Gnomad ASJ AF: 0.293

Gnomad EAS AF: 0.0897

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.188

Gnomad MID AF: 0.316

Gnomad NFE AF: 0.206

Gnomad OTH AF: 0.293

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

GnomAD4 genome AF: 0.279 AC: 42386 AN: 152162 Hom.: 6831 Cov.: 33 AF XY: 0.275 AC XY: 20474 AN XY: 74400

African (AFR) AF: 0.441 AC: 18295 AN: 41520

American (AMR) AF: 0.327 AC: 5000 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.293 AC: 1015 AN: 3470

East Asian (EAS) AF: 0.0905 AC: 468 AN: 5170

South Asian (SAS) AF: 0.141 AC: 679 AN: 4830

European-Finnish (FIN) AF: 0.188 AC: 1993 AN: 10580

Middle Eastern (MID) AF: 0.313 AC: 92 AN: 294

European-Non Finnish (NFE) AF: 0.206 AC: 14037 AN: 67984

Other (OTH) AF: 0.291 AC: 615 AN: 2114

Alfa AF: 0.246 Hom.: 868

Bravo AF: 0.298

Asia WGS AF: 0.146 AC: 506 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.76
CADD	Benign	12
DANN	Benign	0.66
PhyloP100		0.036

Splicing

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

Other links and lift over

dbSNP: rs35996865; hg19: chr18-18692344;