7-47036178-G-C

Variant names:

• chr7-47036178-G-C
• rs12668095
• ENST00000412996.2:n.114-9755C>G

Variant summary

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

The ENST00000412996.2(ENSG00000229192):​n.114-9755C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.106 in 152,188 control chromosomes in the GnomAD database, including 1,008 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 0.11 (1008 hom., cov: 32)
• Consequence: ENSG00000229192 ENST00000412996.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.198
• Publications: 4 publications found

Genes affected

ENSG00000229192 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000412996.2. 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
	ENSG00000229192	ENST00000412996.2	TSL:3	n.114-9755C>G		intron	N/A
	ENSG00000232072	ENST00000433337.1	TSL:3	n.237+13264C>G		intron	N/A
	ENSG00000229192	ENST00000455078.5	TSL:3	n.134+1781C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16142 AN: 152070 Hom.: 1010 Cov.: 32

Gnomad AFR AF: 0.0692

Gnomad AMI AF: 0.130

Gnomad AMR AF: 0.123

Gnomad ASJ AF: 0.122

Gnomad EAS AF: 0.244

Gnomad SAS AF: 0.0878

Gnomad FIN AF: 0.194

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.0960

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

GnomAD4 genome AF: 0.106 AC: 16138 AN: 152188 Hom.: 1008 Cov.: 32 AF XY: 0.111 AC XY: 8232 AN XY: 74394

African (AFR) AF: 0.0692 AC: 2876 AN: 41556

American (AMR) AF: 0.123 AC: 1881 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.122 AC: 423 AN: 3472

East Asian (EAS) AF: 0.243 AC: 1257 AN: 5170

South Asian (SAS) AF: 0.0877 AC: 422 AN: 4812

European-Finnish (FIN) AF: 0.194 AC: 2048 AN: 10578

Middle Eastern (MID) AF: 0.0782 AC: 23 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6888 AN: 67988

Other (OTH) AF: 0.0950 AC: 201 AN: 2116

Alfa AF: 0.0632 Hom.: 92

Bravo AF: 0.102

Asia WGS AF: 0.143 AC: 497 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.80
DANN	Benign	0.69
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs12668095; hg19: chr7-47075776;