chr20-23996435-A-G

Variant names:

• chr20-23996435-A-G
• rs3887942
• ENST00000846978.1:n.264T>C

Variant summary

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

The ENST00000846978.1(ENSG00000310076):​n.264T>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 0.287 in 151,674 control chromosomes in the GnomAD database, including 8,022 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 0.29 (8022 hom., cov: 32)
• Consequence: ENSG00000310076 ENST00000846978.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.627
• Publications: 2 publications found

Genes affected

ENSG00000310076 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.521 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000846978.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000310076	ENST00000846978.1		n.264T>C		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000310043	ENST00000846737.1		n.111-21A>G		intron	N/A
	ENSG00000310043	ENST00000846738.1		n.392-18A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.286 AC: 43402 AN: 151556 Hom.: 7993 Cov.: 32

Gnomad AFR AF: 0.526

Gnomad AMI AF: 0.207

Gnomad AMR AF: 0.214

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.158

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.201

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.287 AC: 43469 AN: 151674 Hom.: 8022 Cov.: 32 AF XY: 0.284 AC XY: 21022 AN XY: 74090

African (AFR) AF: 0.527 AC: 21743 AN: 41272

American (AMR) AF: 0.213 AC: 3245 AN: 15222

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 948 AN: 3472

East Asian (EAS) AF: 0.158 AC: 817 AN: 5168

South Asian (SAS) AF: 0.204 AC: 985 AN: 4820

European-Finnish (FIN) AF: 0.201 AC: 2101 AN: 10448

Middle Eastern (MID) AF: 0.269 AC: 79 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12812 AN: 67962

Other (OTH) AF: 0.261 AC: 551 AN: 2108

Alfa AF: 0.221 Hom.: 6403

Bravo AF: 0.298

Asia WGS AF: 0.214 AC: 747 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.2
DANN	Benign	0.70
PhyloP100		0.63

Splicing

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

Other links and lift over

dbSNP: rs3887942; hg19: chr20-23977072;