rs16970218

Variant names:

• chr19-35316853-A-G
• rs16970218
• ENST00000700969.1:n.190T>C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000700969.1(ENSG00000289845):​n.190T>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 ENST00000700969.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

Genes affected

ENSG00000289845 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000289845	ENST00000700969.1	n.190T>C		non_coding_transcript_exon_variant	Exon 2 of 2

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

Gnomad4 AFR AF: 0.159

Gnomad4 AMR AF: 0.0193

Gnomad4 ASJ AF: 0.0173

Gnomad4 EAS AF: 0.176

Gnomad4 SAS AF: 0.0723

Gnomad4 FIN AF: 0.0119

Gnomad4 NFE AF: 0.00110

Gnomad4 OTH AF: 0.0393

Alfa AF: 0.0474 Hom.: 90

Bravo AF: 0.0600

Asia WGS AF: 0.147 AC: 512 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16970218; hg19: chr19-35807756;