rs2866845

Variant names:

• chr16-13734612-A-G
• rs2866845
• ENST00000573369.5:n.702-4176T>C

Your query was ambiguous. Multiple possible variants found:

• chr16-13734612-A-G
• chr16-13734612-A-T

Variant summary

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

The ENST00000576944.1(ENSG00000262267):​n.384-4176T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,078 control chromosomes in the GnomAD database, including 36,890 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 0.69 (36890 hom., cov: 32)
• Consequence: ENSG00000262267 ENST00000576944.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.62

Genes affected

ENSG00000262267 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.852 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
ENSG00000262267	ENST00000573369.5	n.702-4176T>C		intron_variant	Intron 4 of 4	5
ENSG00000262267	ENST00000576944.1	n.384-4176T>C		intron_variant	Intron 3 of 3	4
ENSG00000262267	ENST00000659657.1	n.335-4176T>C		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.691 AC: 104936 AN: 151960 Hom.: 36886 Cov.: 32

Gnomad AFR AF: 0.565

Gnomad AMI AF: 0.644

Gnomad AMR AF: 0.649

Gnomad ASJ AF: 0.709

Gnomad EAS AF: 0.873

Gnomad SAS AF: 0.708

Gnomad FIN AF: 0.802

Gnomad MID AF: 0.661

Gnomad NFE AF: 0.744

Gnomad OTH AF: 0.683

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

GnomAD4 genome AF: 0.690 AC: 104987 AN: 152078 Hom.: 36890 Cov.: 32 AF XY: 0.694 AC XY: 51614 AN XY: 74330

Gnomad4 AFR AF: 0.565

Gnomad4 AMR AF: 0.649

Gnomad4 ASJ AF: 0.709

Gnomad4 EAS AF: 0.873

Gnomad4 SAS AF: 0.709

Gnomad4 FIN AF: 0.802

Gnomad4 NFE AF: 0.744

Gnomad4 OTH AF: 0.674

Alfa AF: 0.722 Hom.: 23089

Bravo AF: 0.675

Asia WGS AF: 0.720 AC: 2504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	13
DANN	Benign	0.94

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2866845; hg19: chr16-13828469;