16-17937342-C-T

Variant names:

• chr16-17937342-C-T
• rs1019807
• ENST00000569048.5:n.406-4113G>A

Variant summary

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

The ENST00000824815.1(ENSG00000259929):​n.146+30201G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.733 in 152,086 control chromosomes in the GnomAD database, including 41,022 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 0.73 (41022 hom., cov: 32)
• Consequence: ENSG00000259929 ENST00000824815.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.24
• Publications: 2 publications found

Genes affected

ENSG00000259929 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000824815.1. 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
	ENSG00000259929	ENST00000569048.5	TSL:5	n.406-4113G>A		intron	N/A
	ENSG00000259929	ENST00000824815.1		n.146+30201G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.733 AC: 111329 AN: 151968 Hom.: 40983 Cov.: 32

Gnomad AFR AF: 0.818

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.680

Gnomad ASJ AF: 0.699

Gnomad EAS AF: 0.766

Gnomad SAS AF: 0.670

Gnomad FIN AF: 0.638

Gnomad MID AF: 0.712

Gnomad NFE AF: 0.712

Gnomad OTH AF: 0.735

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

GnomAD4 genome AF: 0.733 AC: 111421 AN: 152086 Hom.: 41022 Cov.: 32 AF XY: 0.728 AC XY: 54131 AN XY: 74342

African (AFR) AF: 0.818 AC: 33962 AN: 41520

American (AMR) AF: 0.679 AC: 10378 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.699 AC: 2425 AN: 3470

East Asian (EAS) AF: 0.765 AC: 3951 AN: 5162

South Asian (SAS) AF: 0.671 AC: 3228 AN: 4814

European-Finnish (FIN) AF: 0.638 AC: 6747 AN: 10574

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.712 AC: 48390 AN: 67956

Other (OTH) AF: 0.735 AC: 1552 AN: 2112

Alfa AF: 0.721 Hom.: 20413

Bravo AF: 0.742

Asia WGS AF: 0.720 AC: 2507 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.27
PhyloP100		-1.2

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: rs1019807;

hg19: chr16-18031199;