rs867722

Positions:

• chr20-4071651-G-A

Variant summary

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

The ENST00000379526.1(ENSG00000205300):​n.563+870C>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 0.0817 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: ENST00000379526.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.90

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000379526.1	n.563+870C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.109

Gnomad4 AMR AF: 0.0981

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.389

Gnomad4 SAS AF: 0.0756

Gnomad4 FIN AF: 0.0942

Gnomad4 NFE AF: 0.0405

Gnomad4 OTH AF: 0.0685

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs867722; hg19: chr20-4052298;