16-85943896-G-T

Variant names:

• chr16-85943896-G-T
• rs7202472
• ENST00000645383.1:n.394-1520G>T

Variant summary

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

The ENST00000645383.1(ENSG00000285163):​n.394-1520G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.167 in 152,170 control chromosomes in the GnomAD database, including 2,464 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 0.17 (2464 hom., cov: 32)
• Consequence: ENSG00000285163 ENST00000645383.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.749
• Publications: 6 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=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.206 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.394-1520G>T		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1	n.78-1520G>T		intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646986.2	n.716-1520G>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.167 AC: 25389 AN: 152052 Hom.: 2463 Cov.: 32

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.192

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.0911

Gnomad EAS AF: 0.0919

Gnomad SAS AF: 0.0578

Gnomad FIN AF: 0.272

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.209

Gnomad OTH AF: 0.146

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

GnomAD4 genome AF: 0.167 AC: 25403 AN: 152170 Hom.: 2464 Cov.: 32 AF XY: 0.167 AC XY: 12409 AN XY: 74398

African (AFR) AF: 0.0915 AC: 3802 AN: 41536

American (AMR) AF: 0.195 AC: 2978 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0911 AC: 316 AN: 3470

East Asian (EAS) AF: 0.0921 AC: 478 AN: 5188

South Asian (SAS) AF: 0.0583 AC: 281 AN: 4820

European-Finnish (FIN) AF: 0.272 AC: 2880 AN: 10572

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

European-Non Finnish (NFE) AF: 0.209 AC: 14184 AN: 67996

Other (OTH) AF: 0.144 AC: 304 AN: 2108

Alfa AF: 0.169 Hom.: 1325

Bravo AF: 0.160

Asia WGS AF: 0.0890 AC: 308 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.58
PhyloP100		-0.75

Splicing

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

Other links and lift over

dbSNP: rs7202472; hg19: chr16-85977502;