16-77656966-A-T

Variant names:

• chr16-77656966-A-T
• rs8059387
• ENST00000730964.1:n.117+18007T>A

Variant summary

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

The ENST00000730964.1(ENSG00000295564):​n.117+18007T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.887 in 152,196 control chromosomes in the GnomAD database, including 59,900 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 0.89 (59900 hom., cov: 32)
• Consequence: ENSG00000295564 ENST00000730964.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.171
• Publications: 1 publications found

Genes affected

ENSG00000295564 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.925 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
ENSG00000295564	ENST00000730964.1	n.117+18007T>A		intron_variant	Intron 1 of 2
ENSG00000278862	ENST00000624623.1	n.-208A>T		upstream_gene_variant		6
ENSG00000295605	ENST00000731291.1	n.-202A>T		upstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.887 AC: 134829 AN: 152078 Hom.: 59856 Cov.: 32

Gnomad AFR AF: 0.933

Gnomad AMI AF: 0.811

Gnomad AMR AF: 0.886

Gnomad ASJ AF: 0.883

Gnomad EAS AF: 0.911

Gnomad SAS AF: 0.857

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.915

Gnomad NFE AF: 0.860

Gnomad OTH AF: 0.899

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

GnomAD4 genome AF: 0.887 AC: 134931 AN: 152196 Hom.: 59900 Cov.: 32 AF XY: 0.886 AC XY: 65955 AN XY: 74414

African (AFR) AF: 0.933 AC: 38748 AN: 41526

American (AMR) AF: 0.887 AC: 13561 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.883 AC: 3063 AN: 3470

East Asian (EAS) AF: 0.912 AC: 4694 AN: 5148

South Asian (SAS) AF: 0.856 AC: 4130 AN: 4822

European-Finnish (FIN) AF: 0.881 AC: 9344 AN: 10602

Middle Eastern (MID) AF: 0.905 AC: 266 AN: 294

European-Non Finnish (NFE) AF: 0.860 AC: 58487 AN: 68012

Other (OTH) AF: 0.898 AC: 1898 AN: 2114

Alfa AF: 0.812 Hom.: 2416

Bravo AF: 0.893

Asia WGS AF: 0.898 AC: 3126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	2.4
DANN	Benign	0.57
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs8059387; hg19: chr16-77690863;