chr16-85941535-G-A

Variant names:

• chr16-85941535-G-A
• rs4843869
• ENST00000645383.1:n.394-3881G>A

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.394-3881G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.175 in 152,122 control chromosomes in the GnomAD database, including 2,734 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 0.18 (2734 hom., cov: 31)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.15
• Publications: 3 publications found

Genes affected

ENSG00000285163 (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 (NFE) allele frequency at 95% confidence interval = 0.22 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
ENSG00000285163	ENST00000645383.1	n.394-3881G>A		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1	n.78-3881G>A		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646986.2	n.716-3881G>A		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.175 AC: 26624 AN: 152004 Hom.: 2733 Cov.: 31

Gnomad AFR AF: 0.0944

Gnomad AMI AF: 0.116

Gnomad AMR AF: 0.200

Gnomad ASJ AF: 0.0914

Gnomad EAS AF: 0.0876

Gnomad SAS AF: 0.0679

Gnomad FIN AF: 0.282

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.223

Gnomad OTH AF: 0.157

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

GnomAD4 genome AF: 0.175 AC: 26638 AN: 152122 Hom.: 2734 Cov.: 31 AF XY: 0.175 AC XY: 12985 AN XY: 74354

African (AFR) AF: 0.0942 AC: 3911 AN: 41512

American (AMR) AF: 0.201 AC: 3072 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.0914 AC: 317 AN: 3470

East Asian (EAS) AF: 0.0878 AC: 454 AN: 5172

South Asian (SAS) AF: 0.0684 AC: 330 AN: 4828

European-Finnish (FIN) AF: 0.282 AC: 2979 AN: 10548

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.223 AC: 15136 AN: 67996

Other (OTH) AF: 0.155 AC: 327 AN: 2110

Alfa AF: 0.191 Hom.: 710

Bravo AF: 0.167

Asia WGS AF: 0.0880 AC: 307 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	2.1
DANN	Benign	0.50
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs4843869; hg19: chr16-85975141;