7-136798723-T-C

Variant names:

• chr7-136798723-T-C
• rs7792231
• ENST00000439694.6:n.656-12832A>G

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.656-12832A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.819 in 151,972 control chromosomes in the GnomAD database, including 51,950 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 0.82 (51950 hom., cov: 30)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.142
• Publications: 4 publications found

Genes affected

ENSG00000234352 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.976 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000439694.6. 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
	ENSG00000234352	ENST00000439694.6	TSL:1	n.656-12832A>G		intron	N/A
	ENSG00000234352	ENST00000586239.5	TSL:5	n.274-12832A>G		intron	N/A
	ENSG00000234352	ENST00000592183.5	TSL:4	n.475-12832A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.819 AC: 124335 AN: 151854 Hom.: 51915 Cov.: 30

Gnomad AFR AF: 0.629

Gnomad AMI AF: 0.864

Gnomad AMR AF: 0.897

Gnomad ASJ AF: 0.901

Gnomad EAS AF: 0.998

Gnomad SAS AF: 0.938

Gnomad FIN AF: 0.863

Gnomad MID AF: 0.889

Gnomad NFE AF: 0.881

Gnomad OTH AF: 0.843

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

GnomAD4 genome AF: 0.819 AC: 124427 AN: 151972 Hom.: 51950 Cov.: 30 AF XY: 0.821 AC XY: 61031 AN XY: 74308

African (AFR) AF: 0.630 AC: 26079 AN: 41412

American (AMR) AF: 0.898 AC: 13683 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.901 AC: 3128 AN: 3470

East Asian (EAS) AF: 0.998 AC: 5154 AN: 5162

South Asian (SAS) AF: 0.939 AC: 4532 AN: 4828

European-Finnish (FIN) AF: 0.863 AC: 9130 AN: 10580

Middle Eastern (MID) AF: 0.887 AC: 259 AN: 292

European-Non Finnish (NFE) AF: 0.881 AC: 59893 AN: 67964

Other (OTH) AF: 0.845 AC: 1781 AN: 2108

Alfa AF: 0.861 Hom.: 25441

Bravo AF: 0.812

Asia WGS AF: 0.957 AC: 3328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.59
PhyloP100		0.14

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7792231;

hg19: chr7-136483470;