rs867722

Variant names:

• chr20-4071651-G-A
• rs867722
• ENST00000379526.1:n.563+870C>T

Variant summary

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

The ENST00000379526.1(ENSG00000205300):​n.563+870C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0817 in 152,208 control chromosomes in the GnomAD database, including 851 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 0.082 (851 hom., cov: 32)
• Consequence: ENSG00000205300 ENST00000379526.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90
• Publications: 1 publications found

Genes affected

ENSG00000205300 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.375 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
ENSG00000205300	ENST00000379526.1	n.563+870C>T		intron_variant	Intron 2 of 2	3
ENSG00000205300	ENST00000792227.1	n.261+870C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.0816 AC: 12418 AN: 152090 Hom.: 851 Cov.: 32

Gnomad AFR AF: 0.109

Gnomad AMI AF: 0.0835

Gnomad AMR AF: 0.0983

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.390

Gnomad SAS AF: 0.0756

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.0380

Gnomad NFE AF: 0.0406

Gnomad OTH AF: 0.0688

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

GnomAD4 genome AF: 0.0817 AC: 12432 AN: 152208 Hom.: 851 Cov.: 32 AF XY: 0.0850 AC XY: 6326 AN XY: 74418

African (AFR) AF: 0.109 AC: 4517 AN: 41528

American (AMR) AF: 0.0981 AC: 1502 AN: 15304

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3472

East Asian (EAS) AF: 0.389 AC: 2000 AN: 5138

South Asian (SAS) AF: 0.0756 AC: 365 AN: 4826

European-Finnish (FIN) AF: 0.0942 AC: 999 AN: 10604

Middle Eastern (MID) AF: 0.0340 AC: 10 AN: 294

European-Non Finnish (NFE) AF: 0.0405 AC: 2758 AN: 68016

Other (OTH) AF: 0.0685 AC: 145 AN: 2116

Alfa AF: 0.0622 Hom.: 55

Bravo AF: 0.0871

Asia WGS AF: 0.182 AC: 635 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	13
DANN	Benign	0.75
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs867722; hg19: chr20-4052298;