XR_007063406.1:n.222-6678T>C

Variant names:

• chr12-92604738-A-G
• rs17730330
• ENST00000836767.1:n.270-6678T>C

Variant summary

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

The XR_007063406.1(LOC124902983):​n.222-6678T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 152,124 control chromosomes in the GnomAD database, including 482 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 0.078 (482 hom., cov: 32)
• Consequence: LOC124902983 XR_007063406.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74
• Publications: 4 publications found

Genes affected

ENSG00000308842 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000836767.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308842	ENST00000836767.1		n.270-6678T>C		intron	N/A
	ENSG00000308842	ENST00000836768.1		n.348-6678T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0779 AC: 11838 AN: 152006 Hom.: 483 Cov.: 32

Gnomad AFR AF: 0.0873

Gnomad AMI AF: 0.0351

Gnomad AMR AF: 0.0503

Gnomad ASJ AF: 0.0542

Gnomad EAS AF: 0.0576

Gnomad SAS AF: 0.137

Gnomad FIN AF: 0.0858

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.0765

Gnomad OTH AF: 0.0644

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

GnomAD4 genome AF: 0.0778 AC: 11836 AN: 152124 Hom.: 482 Cov.: 32 AF XY: 0.0781 AC XY: 5805 AN XY: 74360

African (AFR) AF: 0.0871 AC: 3614 AN: 41500

American (AMR) AF: 0.0502 AC: 766 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0542 AC: 188 AN: 3470

East Asian (EAS) AF: 0.0577 AC: 299 AN: 5180

South Asian (SAS) AF: 0.137 AC: 658 AN: 4810

European-Finnish (FIN) AF: 0.0858 AC: 908 AN: 10582

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.0765 AC: 5205 AN: 68006

Other (OTH) AF: 0.0637 AC: 134 AN: 2104

Alfa AF: 0.0764 Hom.: 70

Bravo AF: 0.0716

Asia WGS AF: 0.0820 AC: 285 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.43
DANN	Benign	0.48
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs17730330; hg19: chr12-92998514;