rs969921

Variant names:

• chr20-21966546-A-T
• rs969921
• ENST00000438222.1:n.57-3725A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000438222.1(ENSG00000238034):​n.57-3725A>T variant causes a intron 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: ENSG00000238034 ENST00000438222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.501
• Publications: 5 publications found

Genes affected

ENSG00000238034 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000238034	ENST00000438222.1	n.57-3725A>T		intron_variant	Intron 1 of 1	3
ENSG00000238034	ENST00000686630.2	n.241-3725A>T		intron_variant	Intron 2 of 2
ENSG00000238034	ENST00000779696.1	n.218-3725A>T		intron_variant	Intron 2 of 2

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

African (AFR) AF: 0.292 AC: 12096 AN: 41428

American (AMR) AF: 0.587 AC: 8942 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.467 AC: 1620 AN: 3472

East Asian (EAS) AF: 0.504 AC: 2595 AN: 5144

South Asian (SAS) AF: 0.512 AC: 2469 AN: 4822

European-Finnish (FIN) AF: 0.375 AC: 3957 AN: 10544

Middle Eastern (MID) AF: 0.544 AC: 160 AN: 294

European-Non Finnish (NFE) AF: 0.445 AC: 30234 AN: 67874

Other (OTH) AF: 0.471 AC: 991 AN: 2104

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
PhyloP100		-0.50

Splicing

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

Other links and lift over

dbSNP: rs969921; hg19: chr20-21947184;