chr16-85938234-C-G

Variant names:

• chr16-85938234-C-G
• rs305067
• ENST00000645383.1:n.393+5960C>G

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.393+5960C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.751 in 152,092 control chromosomes in the GnomAD database, including 44,080 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 0.75 (44080 hom., cov: 31)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.829
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.906 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645383.1. 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
	ENSG00000285163	ENST00000645383.1		n.393+5960C>G		intron	N/A
	ENSG00000285163	ENST00000646214.1		n.78-7182C>G		intron	N/A
	ENSG00000285163	ENST00000646986.2		n.715+2223C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.751 AC: 114121 AN: 151974 Hom.: 44013 Cov.: 31

Gnomad AFR AF: 0.914

Gnomad AMI AF: 0.686

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.865

Gnomad SAS AF: 0.770

Gnomad FIN AF: 0.784

Gnomad MID AF: 0.551

Gnomad NFE AF: 0.648

Gnomad OTH AF: 0.693

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

GnomAD4 genome AF: 0.751 AC: 114255 AN: 152092 Hom.: 44080 Cov.: 31 AF XY: 0.757 AC XY: 56305 AN XY: 74332

African (AFR) AF: 0.914 AC: 37953 AN: 41516

American (AMR) AF: 0.748 AC: 11432 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.598 AC: 2076 AN: 3472

East Asian (EAS) AF: 0.866 AC: 4470 AN: 5162

South Asian (SAS) AF: 0.771 AC: 3714 AN: 4820

European-Finnish (FIN) AF: 0.784 AC: 8301 AN: 10586

Middle Eastern (MID) AF: 0.548 AC: 161 AN: 294

European-Non Finnish (NFE) AF: 0.648 AC: 44054 AN: 67936

Other (OTH) AF: 0.695 AC: 1470 AN: 2114

Alfa AF: 0.706 Hom.: 4568

Bravo AF: 0.754

Asia WGS AF: 0.833 AC: 2892 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.3
DANN	Benign	0.53
PhyloP100		-0.83

Splicing

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

Other links and lift over

dbSNP: rs305067; hg19: chr16-85971840;