chr7-33063693-A-C

Variant names:

• chr7-33063693-A-C
• rs34307182
• ENST00000788220.1:n.124+691A>C

Variant summary

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

The ENST00000788220.1(ENSG00000302625):​n.124+691A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.304 in 152,130 control chromosomes in the GnomAD database, including 7,375 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 0.30 (7375 hom., cov: 32)
• Consequence: ENSG00000302625 ENST00000788220.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 2 publications found

Genes affected

ENSG00000302625 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.411 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000788220.1. 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
	ENSG00000302625	ENST00000788220.1		n.124+691A>C		intron	N/A
	ENSG00000302625	ENST00000788221.1		n.486+299A>C		intron	N/A
	ENSG00000302625	ENST00000788222.1		n.478+45A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.304 AC: 46188 AN: 152012 Hom.: 7369 Cov.: 32

Gnomad AFR AF: 0.226

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.419

Gnomad ASJ AF: 0.296

Gnomad EAS AF: 0.210

Gnomad SAS AF: 0.246

Gnomad FIN AF: 0.347

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.329

Gnomad OTH AF: 0.325

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

GnomAD4 genome AF: 0.304 AC: 46217 AN: 152130 Hom.: 7375 Cov.: 32 AF XY: 0.306 AC XY: 22750 AN XY: 74362

African (AFR) AF: 0.226 AC: 9382 AN: 41504

American (AMR) AF: 0.419 AC: 6408 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.296 AC: 1027 AN: 3468

East Asian (EAS) AF: 0.210 AC: 1089 AN: 5180

South Asian (SAS) AF: 0.248 AC: 1195 AN: 4822

European-Finnish (FIN) AF: 0.347 AC: 3675 AN: 10576

Middle Eastern (MID) AF: 0.316 AC: 93 AN: 294

European-Non Finnish (NFE) AF: 0.329 AC: 22393 AN: 67980

Other (OTH) AF: 0.321 AC: 678 AN: 2114

Alfa AF: 0.307 Hom.: 1050

Bravo AF: 0.307

Asia WGS AF: 0.223 AC: 777 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	3.0
DANN	Benign	0.67
PhyloP100		0.35

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: rs34307182;

hg19: chr7-33103305;