rs16997921

Positions:

• chr4-126724591-C-T

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, non coding transcript 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: ENST00000661809.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.02

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000661809.1	n.99+10834G>A		intron_variant, non_coding_transcript_variant

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;