rs6992112

Variant names:

• chr8-16787646-T-A
• rs6992112
• ENST00000521411.2:n.279-4364A>T

Your query was ambiguous. Multiple possible variants found:

• chr8-16787646-T-A
• chr8-16787646-T-G

Variant summary

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

The ENST00000521411.2(ENSG00000253496):​n.279-4364A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.904 in 152,214 control chromosomes in the GnomAD database, including 62,798 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 0.90 (62798 hom., cov: 32)
• Consequence: ENSG00000253496 ENST00000521411.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.02
• Publications: 0 publications found

Genes affected

ENSG00000253496 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.959 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105379297	XR_949525.1	n.158-4364A>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000253496	ENST00000521411.2	n.279-4364A>T		intron_variant	Intron 2 of 3	5
ENSG00000253496	ENST00000755781.1	n.229-4364A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.904 AC: 137541 AN: 152096 Hom.: 62783 Cov.: 32

Gnomad AFR AF: 0.771

Gnomad AMI AF: 0.999

Gnomad AMR AF: 0.942

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.859

Gnomad SAS AF: 0.919

Gnomad FIN AF: 0.963

Gnomad MID AF: 0.911

Gnomad NFE AF: 0.966

Gnomad OTH AF: 0.926

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

GnomAD4 genome AF: 0.904 AC: 137604 AN: 152214 Hom.: 62798 Cov.: 32 AF XY: 0.904 AC XY: 67303 AN XY: 74418

African (AFR) AF: 0.771 AC: 31983 AN: 41496

American (AMR) AF: 0.942 AC: 14405 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3292 AN: 3472

East Asian (EAS) AF: 0.858 AC: 4437 AN: 5170

South Asian (SAS) AF: 0.919 AC: 4440 AN: 4830

European-Finnish (FIN) AF: 0.963 AC: 10217 AN: 10610

Middle Eastern (MID) AF: 0.908 AC: 267 AN: 294

European-Non Finnish (NFE) AF: 0.966 AC: 65703 AN: 68040

Other (OTH) AF: 0.928 AC: 1961 AN: 2114

Alfa AF: 0.928 Hom.: 8192

Bravo AF: 0.896

Asia WGS AF: 0.903 AC: 3140 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	6.8
DANN	Benign	0.81
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs6992112; hg19: chr8-16645155;