16-72083852-C-T

Variant names:

• chr16-72083852-C-T
• rs152837
• ENST00000562153.6:n.284+5135G>A

Variant summary

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

The ENST00000562153.6(ENSG00000310525):​n.284+5135G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.954 in 152,314 control chromosomes in the GnomAD database, including 69,368 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 0.95 (69368 hom., cov: 33)
• Consequence: ENSG00000310525 ENST00000562153.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.24
• Publications: 7 publications found

Genes affected

ENSG00000310525 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.979 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
ENSG00000310525	ENST00000562153.6	n.284+5135G>A		intron_variant	Intron 3 of 5	4		ENSP00000454635.2

Frequencies

GnomAD3 genomes AF: 0.954 AC: 145179 AN: 152196 Hom.: 69308 Cov.: 33

Gnomad AFR AF: 0.987

Gnomad AMI AF: 0.939

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.968

Gnomad EAS AF: 1.00

Gnomad SAS AF: 0.989

Gnomad FIN AF: 0.948

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.927

Gnomad OTH AF: 0.945

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

GnomAD4 genome AF: 0.954 AC: 145298 AN: 152314 Hom.: 69368 Cov.: 33 AF XY: 0.956 AC XY: 71195 AN XY: 74468

African (AFR) AF: 0.987 AC: 41010 AN: 41564

American (AMR) AF: 0.963 AC: 14743 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.968 AC: 3362 AN: 3472

East Asian (EAS) AF: 1.00 AC: 5185 AN: 5186

South Asian (SAS) AF: 0.989 AC: 4767 AN: 4822

European-Finnish (FIN) AF: 0.948 AC: 10062 AN: 10614

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.927 AC: 63046 AN: 68034

Other (OTH) AF: 0.946 AC: 1999 AN: 2114

Alfa AF: 0.937 Hom.: 125528

Bravo AF: 0.957

Asia WGS AF: 0.992 AC: 3447 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.45
DANN	Benign	0.70
PhyloP100		-2.2

Splicing

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

Other links and lift over

dbSNP: rs152837; hg19: chr16-72117751;