20-38720715-G-T

Variant names:

• chr20-38720715-G-T
• rs6092933
• ENST00000780561.1:n.437+2982C>A

Variant summary

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

The ENST00000780561.1(ENSG00000301653):​n.437+2982C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 151,472 control chromosomes in the GnomAD database, including 3,526 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 0.21 (3526 hom., cov: 30)
• Consequence: ENSG00000301653 ENST00000780561.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.307
• Publications: 2 publications found

Genes affected

ENSG00000301653 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.244 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
ENSG00000301653	ENST00000780561.1	n.437+2982C>A		intron_variant	Intron 1 of 2
ENSG00000301653	ENST00000780562.1	n.397+2982C>A		intron_variant	Intron 1 of 1
ENSG00000301653	ENST00000780563.1	n.318+2982C>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.212 AC: 32018 AN: 151354 Hom.: 3517 Cov.: 30

Gnomad AFR AF: 0.206

Gnomad AMI AF: 0.303

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.215

Gnomad EAS AF: 0.0991

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.265

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.217

Gnomad OTH AF: 0.227

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

GnomAD4 genome AF: 0.212 AC: 32047 AN: 151472 Hom.: 3526 Cov.: 30 AF XY: 0.216 AC XY: 15985 AN XY: 73974

African (AFR) AF: 0.206 AC: 8508 AN: 41250

American (AMR) AF: 0.182 AC: 2764 AN: 15228

Ashkenazi Jewish (ASJ) AF: 0.215 AC: 743 AN: 3460

East Asian (EAS) AF: 0.0988 AC: 507 AN: 5134

South Asian (SAS) AF: 0.256 AC: 1222 AN: 4774

European-Finnish (FIN) AF: 0.265 AC: 2784 AN: 10500

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.217 AC: 14691 AN: 67828

Other (OTH) AF: 0.225 AC: 473 AN: 2102

Alfa AF: 0.145 Hom.: 341

Bravo AF: 0.198

Asia WGS AF: 0.202 AC: 701 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.8
DANN	Benign	0.41
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs6092933; hg19: chr20-37349358;