rs17749681

Variant names:

• chr16-9713930-T-C
• rs17749681
• ENST00000753716.1:n.55-2801T>C

Variant summary

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

The ENST00000753716.1(ENSG00000298185):​n.55-2801T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 151,928 control chromosomes in the GnomAD database, including 13,069 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 0.41 (13069 hom., cov: 31)
• Consequence: ENSG00000298185 ENST00000753716.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41
• Publications: 6 publications found

Genes affected

ENSG00000298185 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000753716.1. 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
	ENSG00000298185	ENST00000753716.1		n.55-2801T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.412 AC: 62528 AN: 151810 Hom.: 13057 Cov.: 31

Gnomad AFR AF: 0.397

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.520

Gnomad EAS AF: 0.479

Gnomad SAS AF: 0.563

Gnomad FIN AF: 0.385

Gnomad MID AF: 0.429

Gnomad NFE AF: 0.413

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.412 AC: 62577 AN: 151928 Hom.: 13069 Cov.: 31 AF XY: 0.415 AC XY: 30815 AN XY: 74260

African (AFR) AF: 0.397 AC: 16450 AN: 41420

American (AMR) AF: 0.367 AC: 5603 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.520 AC: 1806 AN: 3470

East Asian (EAS) AF: 0.478 AC: 2459 AN: 5142

South Asian (SAS) AF: 0.562 AC: 2701 AN: 4808

European-Finnish (FIN) AF: 0.385 AC: 4076 AN: 10576

Middle Eastern (MID) AF: 0.431 AC: 125 AN: 290

European-Non Finnish (NFE) AF: 0.413 AC: 28026 AN: 67934

Other (OTH) AF: 0.449 AC: 946 AN: 2106

Alfa AF: 0.421 Hom.: 8934

Bravo AF: 0.406

Asia WGS AF: 0.518 AC: 1801 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.44
DANN	Benign	0.25
PhyloP100		-1.4

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: rs17749681;

hg19: chr16-9807787;