rs7797223

Variant names:

• chr7-136863156-A-T
• rs7797223
• ENST00000439694.6:n.656-77265T>A

Variant summary

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

The ENST00000439694.6(ENSG00000234352):​n.656-77265T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 152,158 control chromosomes in the GnomAD database, including 4,990 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 0.25 (4990 hom., cov: 33)
• Consequence: ENSG00000234352 ENST00000439694.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 1 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 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.656-77265T>A		intron	N/A
	ENSG00000234352	ENST00000586239.5	TSL:5	n.274-77265T>A		intron	N/A
	ENSG00000234352	ENST00000592183.5	TSL:4	n.475-77265T>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37313 AN: 152040 Hom.: 4984 Cov.: 33

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.340

Gnomad AMR AF: 0.194

Gnomad ASJ AF: 0.211

Gnomad EAS AF: 0.0121

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.190

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.248

Gnomad OTH AF: 0.229

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

GnomAD4 genome AF: 0.245 AC: 37337 AN: 152158 Hom.: 4990 Cov.: 33 AF XY: 0.237 AC XY: 17647 AN XY: 74382

African (AFR) AF: 0.320 AC: 13257 AN: 41492

American (AMR) AF: 0.194 AC: 2958 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.211 AC: 731 AN: 3472

East Asian (EAS) AF: 0.0120 AC: 62 AN: 5182

South Asian (SAS) AF: 0.123 AC: 592 AN: 4824

European-Finnish (FIN) AF: 0.190 AC: 2007 AN: 10582

Middle Eastern (MID) AF: 0.218 AC: 64 AN: 294

European-Non Finnish (NFE) AF: 0.248 AC: 16878 AN: 68014

Other (OTH) AF: 0.227 AC: 479 AN: 2112

Alfa AF: 0.250 Hom.: 617

Bravo AF: 0.249

Asia WGS AF: 0.0760 AC: 266 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.5
DANN	Benign	0.38
PhyloP100		-0.077

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: rs7797223;

hg19: chr7-136547903;