rs35996865

Variant names:

• chr18-21112383-T-G
• rs35996865

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0360

ACMG classification

Verdict is Benign. Variant got -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

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

Gnomad4 AFR AF: 0.441

Gnomad4 AMR AF: 0.327

Gnomad4 ASJ AF: 0.293

Gnomad4 EAS AF: 0.0905

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.188

Gnomad4 NFE AF: 0.206

Gnomad4 OTH AF: 0.291

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs35996865; hg19: chr18-18692344;