16-78019746-A-T

Variant names:

• chr16-78019746-A-T
• rs2735413
• ENST00000563114.1:n.42-4617T>A

Variant summary

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

The ENST00000563114.1(ENSG00000261540):​n.42-4617T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.63 in 152,082 control chromosomes in the GnomAD database, including 32,464 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 0.63 (32464 hom., cov: 32)
• Consequence: ENSG00000261540 ENST00000563114.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.146
• Publications: 5 publications found

Genes affected

ENSG00000261540 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000563114.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261540	ENST00000563114.1	TSL:1	n.42-4617T>A		intron	N/A
	ENSG00000261540	ENST00000767192.1		n.187-2568T>A		intron	N/A
	ENSG00000261540	ENST00000767193.1		n.80-1263T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.630 AC: 95697 AN: 151964 Hom.: 32448 Cov.: 32

Gnomad AFR AF: 0.355

Gnomad AMI AF: 0.825

Gnomad AMR AF: 0.692

Gnomad ASJ AF: 0.678

Gnomad EAS AF: 0.692

Gnomad SAS AF: 0.788

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.737

Gnomad OTH AF: 0.664

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

GnomAD4 genome AF: 0.630 AC: 95747 AN: 152082 Hom.: 32464 Cov.: 32 AF XY: 0.635 AC XY: 47238 AN XY: 74352

African (AFR) AF: 0.355 AC: 14754 AN: 41504

American (AMR) AF: 0.692 AC: 10575 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.678 AC: 2354 AN: 3470

East Asian (EAS) AF: 0.691 AC: 3566 AN: 5162

South Asian (SAS) AF: 0.788 AC: 3799 AN: 4820

European-Finnish (FIN) AF: 0.781 AC: 8264 AN: 10578

Middle Eastern (MID) AF: 0.675 AC: 197 AN: 292

European-Non Finnish (NFE) AF: 0.737 AC: 50078 AN: 67960

Other (OTH) AF: 0.667 AC: 1409 AN: 2114

Alfa AF: 0.574 Hom.: 1891

Bravo AF: 0.610

Asia WGS AF: 0.740 AC: 2568 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.97
DANN	Benign	0.13
PhyloP100		-0.15

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2735413;

hg19: chr16-78053643;