rs16970218

Variant names:

• chr19-35316853-A-G
• rs16970218
• ENST00000700969.2:n.296T>C

Variant summary

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

The ENST00000700969.2(ENSG00000289845):​n.296T>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 0.0559 in 152,266 control chromosomes in the GnomAD database, including 673 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 0.056 (673 hom., cov: 33)
• Consequence: ENSG00000289845 ENST00000700969.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09
• Publications: 6 publications found

Genes affected

ENSG00000289845 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.167 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000700969.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289845	ENST00000700969.2		n.296T>C		non_coding_transcript_exon	Exon 2 of 2
	ENSG00000289845	ENST00000827650.1		n.232T>C		non_coding_transcript_exon	Exon 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0557 AC: 8468 AN: 152148 Hom.: 669 Cov.: 33

Gnomad AFR AF: 0.159

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0192

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0721

Gnomad FIN AF: 0.0119

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.00110

Gnomad OTH AF: 0.0335

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

GnomAD4 genome AF: 0.0559 AC: 8505 AN: 152266 Hom.: 673 Cov.: 33 AF XY: 0.0563 AC XY: 4194 AN XY: 74454

African (AFR) AF: 0.159 AC: 6599 AN: 41532

American (AMR) AF: 0.0193 AC: 295 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3470

East Asian (EAS) AF: 0.176 AC: 913 AN: 5180

South Asian (SAS) AF: 0.0723 AC: 349 AN: 4824

European-Finnish (FIN) AF: 0.0119 AC: 126 AN: 10618

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.00110 AC: 75 AN: 68024

Other (OTH) AF: 0.0393 AC: 83 AN: 2114

Alfa AF: 0.0638 Hom.: 449

Bravo AF: 0.0600

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.078
DANN	Benign	0.24
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs16970218; hg19: chr19-35807756;