rs16862964

Variant names:

• chr3-188074923-T-C
• rs16862964
• ENST00000754169.1:n.354-184T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-188074923-T-C
• chr3-188074923-T-G

Variant summary

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

The ENST00000754169.1(ENSG00000298263):​n.354-184T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.366 in 151,920 control chromosomes in the GnomAD database, including 10,690 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 0.37 (10690 hom., cov: 31)
• Consequence: ENSG00000298263 ENST00000754169.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.55
• Publications: 9 publications found

Genes affected

ENSG00000298263 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.477 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
ENSG00000298263	ENST00000754169.1	n.354-184T>C		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.366 AC: 55519 AN: 151802 Hom.: 10681 Cov.: 31

Gnomad AFR AF: 0.483

Gnomad AMI AF: 0.198

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.419

Gnomad EAS AF: 0.378

Gnomad SAS AF: 0.354

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.353

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

GnomAD4 genome AF: 0.366 AC: 55570 AN: 151920 Hom.: 10690 Cov.: 31 AF XY: 0.363 AC XY: 26983 AN XY: 74252

African (AFR) AF: 0.483 AC: 19989 AN: 41414

American (AMR) AF: 0.266 AC: 4055 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.419 AC: 1452 AN: 3466

East Asian (EAS) AF: 0.378 AC: 1950 AN: 5164

South Asian (SAS) AF: 0.353 AC: 1699 AN: 4810

European-Finnish (FIN) AF: 0.318 AC: 3349 AN: 10540

Middle Eastern (MID) AF: 0.503 AC: 148 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22008 AN: 67952

Other (OTH) AF: 0.352 AC: 740 AN: 2104

Alfa AF: 0.344 Hom.: 14461

Bravo AF: 0.364

Asia WGS AF: 0.325 AC: 1132 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	0.074
DANN	Benign	0.26
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs16862964; hg19: chr3-187792711;