rs16866493

Variant names:

• chr2-7843938-T-C
• rs16866493
• ENST00000815075.1:n.184A>G

Variant summary

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

The ENST00000815075.1(ENSG00000226506):​n.184A>G 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 0.0756 in 152,280 control chromosomes in the GnomAD database, including 1,278 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 0.076 (1278 hom., cov: 32)
• Consequence: ENSG00000226506 ENST00000815075.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.16
• Publications: 2 publications found

Genes affected

ENSG00000226506 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.24 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105373408	XR_922750.1	n.94-15402A>G		intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000226506	ENST00000815075.1	n.184A>G		non_coding_transcript_exon_variant	Exon 2 of 2
ENSG00000226506	ENST00000815071.1	n.120-15402A>G		intron_variant	Intron 1 of 3
ENSG00000226506	ENST00000815072.1	n.337+2508A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.0754 AC: 11478 AN: 152162 Hom.: 1276 Cov.: 32

Gnomad AFR AF: 0.244

Gnomad AMI AF: 0.0121

Gnomad AMR AF: 0.0288

Gnomad ASJ AF: 0.0202

Gnomad EAS AF: 0.000192

Gnomad SAS AF: 0.0518

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.00714

Gnomad OTH AF: 0.0559

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

GnomAD4 genome AF: 0.0756 AC: 11512 AN: 152280 Hom.: 1278 Cov.: 32 AF XY: 0.0742 AC XY: 5528 AN XY: 74468

African (AFR) AF: 0.244 AC: 10130 AN: 41532

American (AMR) AF: 0.0287 AC: 439 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0202 AC: 70 AN: 3472

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5186

South Asian (SAS) AF: 0.0516 AC: 249 AN: 4826

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10626

Middle Eastern (MID) AF: 0.0272 AC: 8 AN: 294

European-Non Finnish (NFE) AF: 0.00713 AC: 485 AN: 68022

Other (OTH) AF: 0.0553 AC: 117 AN: 2116

Alfa AF: 0.0626 Hom.: 192

Bravo AF: 0.0836

Asia WGS AF: 0.0420 AC: 148 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.098
DANN	Benign	0.33
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs16866493; hg19: chr2-7984069;