rs16842484

Variant names:

• chr1-159677134-T-C
• rs16842484
• ENST00000751816.1:n.107+16445T>C

Variant summary

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

The ENST00000751816.1(ENSG00000297913):​n.107+16445T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.251 in 151,866 control chromosomes in the GnomAD database, including 5,078 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 0.25 (5078 hom., cov: 30)
• Consequence: ENSG00000297913 ENST00000751816.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.212
• Publications: 9 publications found

Genes affected

ENSG00000297913 (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 (AFR) allele frequency at 95% confidence interval = 0.293 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
ENSG00000297913	ENST00000751816.1	n.107+16445T>C		intron_variant	Intron 1 of 2
ENSG00000297913	ENST00000751817.1	n.109+16445T>C		intron_variant	Intron 1 of 3
ENSG00000297913	ENST00000751818.1	n.62+16445T>C		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.251 AC: 38078 AN: 151750 Hom.: 5073 Cov.: 30

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.161

Gnomad AMR AF: 0.182

Gnomad ASJ AF: 0.196

Gnomad EAS AF: 0.00906

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.313

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.260

Gnomad OTH AF: 0.237

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

GnomAD4 genome AF: 0.251 AC: 38112 AN: 151866 Hom.: 5078 Cov.: 30 AF XY: 0.249 AC XY: 18443 AN XY: 74206

African (AFR) AF: 0.297 AC: 12309 AN: 41384

American (AMR) AF: 0.182 AC: 2778 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.196 AC: 680 AN: 3470

East Asian (EAS) AF: 0.00908 AC: 47 AN: 5178

South Asian (SAS) AF: 0.134 AC: 643 AN: 4816

European-Finnish (FIN) AF: 0.313 AC: 3285 AN: 10508

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.260 AC: 17666 AN: 67946

Other (OTH) AF: 0.236 AC: 498 AN: 2110

Alfa AF: 0.253 Hom.: 8468

Bravo AF: 0.245

Asia WGS AF: 0.0970 AC: 342 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.2
DANN	Benign	0.69
PhyloP100		0.21

Splicing

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

Other links and lift over

dbSNP: rs16842484; hg19: chr1-159646924;