rs4843204

Variant names:

• chr16-86993114-T-C
• rs4843204
• ENST00000836704.1:n.85+8826A>G

Variant summary

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

The ENST00000836704.1(ENSG00000289423):​n.85+8826A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0622 in 152,004 control chromosomes in the GnomAD database, including 396 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 0.062 (396 hom., cov: 33)
• Consequence: ENSG00000289423 ENST00000836704.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.734
• Publications: 2 publications found

Genes affected

ENSG00000289423 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.146 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836704.1. 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
	ENSG00000289423	ENST00000836704.1		n.85+8826A>G		intron	N/A
	ENSG00000289423	ENST00000836709.1		n.216-43549A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9432 AN: 151886 Hom.: 389 Cov.: 33

Gnomad AFR AF: 0.0463

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.128

Gnomad ASJ AF: 0.0516

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.0908

Gnomad FIN AF: 0.0816

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0450

Gnomad OTH AF: 0.0711

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

GnomAD4 genome AF: 0.0622 AC: 9462 AN: 152004 Hom.: 396 Cov.: 33 AF XY: 0.0663 AC XY: 4927 AN XY: 74300

African (AFR) AF: 0.0463 AC: 1919 AN: 41442

American (AMR) AF: 0.129 AC: 1971 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0516 AC: 179 AN: 3470

East Asian (EAS) AF: 0.155 AC: 796 AN: 5152

South Asian (SAS) AF: 0.0911 AC: 438 AN: 4808

European-Finnish (FIN) AF: 0.0816 AC: 863 AN: 10578

Middle Eastern (MID) AF: 0.122 AC: 36 AN: 294

European-Non Finnish (NFE) AF: 0.0450 AC: 3061 AN: 67974

Other (OTH) AF: 0.0708 AC: 149 AN: 2104

Alfa AF: 0.0563 Hom.: 104

Bravo AF: 0.0661

Asia WGS AF: 0.107 AC: 371 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.58
DANN	Benign	0.67
PhyloP100		-0.73

Splicing

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

Other links and lift over

dbSNP: rs4843204; hg19: chr16-87026720;