rs969921

chr20-21966546-A-T

Variant summary

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

The ENST00000686630.1(ENSG00000238034):n.195-3725A>T 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 0.418 in 151,836 control chromosomes in the GnomAD database, including 13,959 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 0.42 (13959 hom., cov: 32)
• Consequence: ENST00000686630.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.576 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
	ENST00000686630.1	n.195-3725A>T		intron_variant, non_coding_transcript_variant
	ENST00000438222.1	n.57-3725A>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.418 AC: 63460 AN: 151716 Hom.: 13940 Cov.: 32

Gnomad AFR AF: 0.292

Gnomad AMI AF: 0.490

Gnomad AMR AF: 0.586

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.504

Gnomad SAS AF: 0.513

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.561

Gnomad NFE AF: 0.445

Gnomad OTH AF: 0.464

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

GnomAD4 genome AF: 0.418 AC: 63509 AN: 151836 Hom.: 13959 Cov.: 32 AF XY: 0.418 AC XY: 31023 AN XY: 74150

Gnomad4 AFR AF: 0.292

Gnomad4 AMR AF: 0.587

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.504

Gnomad4 SAS AF: 0.512

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.445

Gnomad4 OTH AF: 0.471

Alfa AF: 0.423 Hom.: 1755

Bravo AF: 0.430

Asia WGS AF: 0.553 AC: 1919 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
Cadd	Benign	4.3
Dann	Benign	0.85

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs969921; hg19: chr20-21947184;