rs16997921

Variant names:

• chr4-126724591-C-T
• rs16997921
• ENST00000661809.1:n.99+10834G>A

Variant summary

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

The ENST00000661809.1(ENSG00000286251):​n.99+10834G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0485 in 152,180 control chromosomes in the GnomAD database, including 206 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 0.049 (206 hom., cov: 32)
• Consequence: ENSG00000286251 ENST00000661809.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.02

Genes affected

ENSG00000286251 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0516 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
ENSG00000286251	ENST00000661809.1	n.99+10834G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes AF: 0.0486 AC: 7383 AN: 152062 Hom.: 206 Cov.: 32

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.0681

Gnomad AMR AF: 0.0391

Gnomad ASJ AF: 0.103

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0381

Gnomad FIN AF: 0.0254

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0530

Gnomad OTH AF: 0.0484

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

GnomAD4 genome AF: 0.0485 AC: 7384 AN: 152180 Hom.: 206 Cov.: 32 AF XY: 0.0466 AC XY: 3469 AN XY: 74396

Gnomad4 AFR AF: 0.0528

Gnomad4 AMR AF: 0.0390

Gnomad4 ASJ AF: 0.103

Gnomad4 EAS AF: 0.000193

Gnomad4 SAS AF: 0.0384

Gnomad4 FIN AF: 0.0254

Gnomad4 NFE AF: 0.0530

Gnomad4 OTH AF: 0.0474

Alfa AF: 0.0517 Hom.: 163

Bravo AF: 0.0488

Asia WGS AF: 0.0180 AC: 63 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.023
DANN	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16997921; hg19: chr4-127645746;