rs892999

Variant names:

• chr6-137817568-G-A
• rs892999
• ENST00000763184.1:n.78G>A

Your query was ambiguous. Multiple possible variants found:

• chr6-137817568-G-A
• chr6-137817568-G-C

Variant summary

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

The ENST00000763184.1(ENSG00000299400):​n.78G>A 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 0.0695 in 152,232 control chromosomes in the GnomAD database, including 390 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 0.069 (390 hom., cov: 32)
• Consequence: ENSG00000299400 ENST00000763184.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.62
• Publications: 6 publications found

Genes affected

ENSG00000299400 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0818 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000763184.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000299400	ENST00000763184.1		n.78G>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000299400	ENST00000763185.1		n.71G>A		non_coding_transcript_exon	Exon 1 of 4
	ENSG00000299400	ENST00000763186.1		n.40G>A		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0695 AC: 10570 AN: 152114 Hom.: 389 Cov.: 32

Gnomad AFR AF: 0.0626

Gnomad AMI AF: 0.0714

Gnomad AMR AF: 0.0464

Gnomad ASJ AF: 0.0605

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0153

Gnomad FIN AF: 0.104

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0836

Gnomad OTH AF: 0.0540

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

GnomAD4 genome AF: 0.0695 AC: 10577 AN: 152232 Hom.: 390 Cov.: 32 AF XY: 0.0686 AC XY: 5109 AN XY: 74428

African (AFR) AF: 0.0626 AC: 2601 AN: 41536

American (AMR) AF: 0.0463 AC: 708 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.0605 AC: 210 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5172

South Asian (SAS) AF: 0.0151 AC: 73 AN: 4820

European-Finnish (FIN) AF: 0.104 AC: 1100 AN: 10610

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0836 AC: 5685 AN: 68010

Other (OTH) AF: 0.0534 AC: 113 AN: 2116

Alfa AF: 0.0574 Hom.: 143

Bravo AF: 0.0656

Asia WGS AF: 0.0160 AC: 58 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.013
DANN	Benign	0.58
PhyloP100		-1.6

Splicing

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

Other links and lift over

dbSNP: rs892999; hg19: chr6-138138705; COSMIC: COSV69428321;