rs16965644

Variant names:

• chr17-40107944-A-G
• rs16965644
• ENST00000800866.1:n.447T>C

Variant summary

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

The ENST00000800866.1(ENSG00000304182):​n.447T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.155 in 152,082 control chromosomes in the GnomAD database, including 2,368 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 0.16 (2368 hom., cov: 31)
• Consequence: ENSG00000304182 ENST00000800866.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.10
• Publications: 12 publications found

Genes affected

ENSG00000304182 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.271 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
ENSG00000304182	ENST00000800866.1	n.447T>C		non_coding_transcript_exon_variant	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.155 AC: 23532 AN: 151964 Hom.: 2354 Cov.: 31

Gnomad AFR AF: 0.275

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.116

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0250

Gnomad FIN AF: 0.0892

Gnomad MID AF: 0.177

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.155 AC: 23585 AN: 152082 Hom.: 2368 Cov.: 31 AF XY: 0.151 AC XY: 11207 AN XY: 74338

African (AFR) AF: 0.276 AC: 11417 AN: 41418

American (AMR) AF: 0.116 AC: 1768 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 363 AN: 3470

East Asian (EAS) AF: 0.000386 AC: 2 AN: 5184

South Asian (SAS) AF: 0.0253 AC: 122 AN: 4830

European-Finnish (FIN) AF: 0.0892 AC: 946 AN: 10602

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8487 AN: 67980

Other (OTH) AF: 0.135 AC: 285 AN: 2104

Alfa AF: 0.138 Hom.: 3297

Bravo AF: 0.164

Asia WGS AF: 0.0370 AC: 130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.39
DANN	Benign	0.74
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs16965644; hg19: chr17-38264197;