chr20-41671593-A-G

Variant names:

• chr20-41671593-A-G
• rs6016596
• ENST00000832335.1:n.405T>C

Variant summary

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

The ENST00000832335.1(ENSG00000288843):​n.405T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.532 in 151,900 control chromosomes in the GnomAD database, including 23,369 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 0.53 (23369 hom., cov: 31)
• Consequence: ENSG00000288843 ENST00000832335.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.370
• Publications: 0 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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.731 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000832335.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000288843	ENST00000832335.1		n.405T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000288843	ENST00000832336.1		n.257T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000288843	ENST00000685138.3		n.272+43861T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80662 AN: 151782 Hom.: 23316 Cov.: 31

Gnomad AFR AF: 0.738

Gnomad AMI AF: 0.363

Gnomad AMR AF: 0.581

Gnomad ASJ AF: 0.395

Gnomad EAS AF: 0.726

Gnomad SAS AF: 0.665

Gnomad FIN AF: 0.372

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.407

Gnomad OTH AF: 0.483

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

GnomAD4 genome AF: 0.532 AC: 80778 AN: 151900 Hom.: 23369 Cov.: 31 AF XY: 0.535 AC XY: 39724 AN XY: 74240

African (AFR) AF: 0.738 AC: 30578 AN: 41428

American (AMR) AF: 0.581 AC: 8866 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.395 AC: 1370 AN: 3470

East Asian (EAS) AF: 0.726 AC: 3730 AN: 5136

South Asian (SAS) AF: 0.664 AC: 3195 AN: 4810

European-Finnish (FIN) AF: 0.372 AC: 3923 AN: 10540

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.407 AC: 27629 AN: 67936

Other (OTH) AF: 0.490 AC: 1030 AN: 2104

Alfa AF: 0.495 Hom.: 2595

Bravo AF: 0.550

Asia WGS AF: 0.747 AC: 2598 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	7.6
DANN	Benign	0.71
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs6016596; hg19: chr20-40300232;