rs1699698

Variant names:

• chr21-24099984-G-A
• rs1699698
• ENST00000668921.1:n.137+14232C>T

Your query was ambiguous. Multiple possible variants found:

• chr21-24099984-G-A
• chr21-24099984-G-T

Variant summary

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

The ENST00000668921.1(ENSG00000287801):​n.137+14232C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0608 in 149,854 control chromosomes in the GnomAD database, including 423 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 0.061 (423 hom., cov: 30)
• Consequence: ENSG00000287801 ENST00000668921.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.03

Genes affected

ENSG00000287801 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.137 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
ENSG00000287801	ENST00000668921.1	n.137+14232C>T		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.0607 AC: 9086 AN: 149764 Hom.: 421 Cov.: 30

Gnomad AFR AF: 0.117

Gnomad AMI AF: 0.0197

Gnomad AMR AF: 0.0654

Gnomad ASJ AF: 0.0172

Gnomad EAS AF: 0.146

Gnomad SAS AF: 0.0525

Gnomad FIN AF: 0.00681

Gnomad MID AF: 0.0226

Gnomad NFE AF: 0.0306

Gnomad OTH AF: 0.0603

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

GnomAD4 genome AF: 0.0608 AC: 9105 AN: 149854 Hom.: 423 Cov.: 30 AF XY: 0.0608 AC XY: 4444 AN XY: 73056

Gnomad4 AFR AF: 0.117

Gnomad4 AMR AF: 0.0655

Gnomad4 ASJ AF: 0.0172

Gnomad4 EAS AF: 0.146

Gnomad4 SAS AF: 0.0528

Gnomad4 FIN AF: 0.00681

Gnomad4 NFE AF: 0.0306

Gnomad4 OTH AF: 0.0592

Alfa AF: 0.00823 Hom.: 3

Bravo AF: 0.0702

Asia WGS AF: 0.0880 AC: 306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.8
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1699698; hg19: chr21-25472297;