chr20-41662167-G-A

Variant names:

• chr20-41662167-G-A
• rs941796
• ENST00000685138.3:n.273-38463C>T

Variant summary

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

The ENST00000685138.3(ENSG00000288843):​n.273-38463C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.519 in 152,042 control chromosomes in the GnomAD database, including 22,278 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 0.52 (22278 hom., cov: 32)
• Consequence: ENSG00000288843 ENST00000685138.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0190
• Publications: 6 publications found

Genes affected

ENSG00000288843 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000685138.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288843	ENST00000685138.3		n.273-38463C>T		intron	N/A
	ENSG00000288843	ENST00000686898.2		n.273-11659C>T		intron	N/A
	ENSG00000288843	ENST00000691734.2		n.404-11659C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.519 AC: 78789 AN: 151924 Hom.: 22231 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.360

Gnomad AMR AF: 0.509

Gnomad ASJ AF: 0.388

Gnomad EAS AF: 0.676

Gnomad SAS AF: 0.662

Gnomad FIN AF: 0.354

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.404

Gnomad OTH AF: 0.468

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

GnomAD4 genome AF: 0.519 AC: 78899 AN: 152042 Hom.: 22278 Cov.: 32 AF XY: 0.521 AC XY: 38759 AN XY: 74332

African (AFR) AF: 0.734 AC: 30454 AN: 41482

American (AMR) AF: 0.509 AC: 7772 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.388 AC: 1348 AN: 3472

East Asian (EAS) AF: 0.676 AC: 3494 AN: 5170

South Asian (SAS) AF: 0.662 AC: 3194 AN: 4824

European-Finnish (FIN) AF: 0.354 AC: 3733 AN: 10546

Middle Eastern (MID) AF: 0.425 AC: 125 AN: 294

European-Non Finnish (NFE) AF: 0.404 AC: 27449 AN: 67960

Other (OTH) AF: 0.474 AC: 1004 AN: 2116

Alfa AF: 0.444 Hom.: 23465

Bravo AF: 0.529

Asia WGS AF: 0.724 AC: 2519 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	3.0
DANN	Benign	0.82
PhyloP100		0.019

Splicing

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

Other links and lift over

dbSNP: rs941796; hg19: chr20-40290806;