rs1699230

Variant names:

• chr20-5865209-G-A
• rs1699230

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 0.618 in 152,010 control chromosomes in the GnomAD database, including 29,356 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 0.62 (29356 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.32

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.702 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: 0.618 AC: 93931 AN: 151892 Hom.: 29348 Cov.: 32

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.509

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.621

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.503

Gnomad NFE AF: 0.570

Gnomad OTH AF: 0.614

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

GnomAD4 genome AF: 0.618 AC: 93993 AN: 152010 Hom.: 29356 Cov.: 32 AF XY: 0.617 AC XY: 45827 AN XY: 74314

Gnomad4 AFR AF: 0.709

Gnomad4 AMR AF: 0.643

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.708

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.542

Gnomad4 NFE AF: 0.570

Gnomad4 OTH AF: 0.615

Alfa AF: 0.574 Hom.: 33853

Bravo AF: 0.631

Asia WGS AF: 0.670 AC: 2329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.051
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: rs1699230; hg19: chr20-5845855;