16-76584018-T-C

Variant names:

• chr16-76584018-T-C
• rs7500366
• ENST00000655556.1:n.3733+30111T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000655556.1(ENSG00000287694):​n.3733+30111T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.51 in 152,112 control chromosomes in the GnomAD database, including 20,396 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 0.51 (20396 hom., cov: 33)
• Consequence: ENSG00000287694 ENST00000655556.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.148

Genes affected

ENSG00000287694 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.584 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
ENSG00000287694	ENST00000655556.1	n.3733+30111T>C		intron_variant	Intron 23 of 24			ENSP00000499374.1
ENSG00000287694	ENST00000563764.2	n.157+30111T>C		intron_variant	Intron 2 of 3	3		ENSP00000455258.1

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77581 AN: 151994 Hom.: 20404 Cov.: 33

Gnomad AFR AF: 0.380

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.530

Gnomad ASJ AF: 0.569

Gnomad EAS AF: 0.602

Gnomad SAS AF: 0.541

Gnomad FIN AF: 0.599

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.509

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

GnomAD4 genome AF: 0.510 AC: 77584 AN: 152112 Hom.: 20396 Cov.: 33 AF XY: 0.513 AC XY: 38187 AN XY: 74368

Gnomad4 AFR AF: 0.379

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.569

Gnomad4 EAS AF: 0.601

Gnomad4 SAS AF: 0.540

Gnomad4 FIN AF: 0.599

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.506

Alfa AF: 0.538 Hom.: 6711

Bravo AF: 0.499

Asia WGS AF: 0.527 AC: 1833 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	3.5
DANN	Benign	0.72

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs7500366; hg19: chr16-76617915;