ENST00000788220.1:n.124+689C>T

Variant names:

• chr7-33063691-C-T
• rs6976843
• ENST00000788220.1:n.124+689C>T

Variant summary

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

The ENST00000788220.1(ENSG00000302625):​n.124+689C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.32 in 152,026 control chromosomes in the GnomAD database, including 8,082 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 0.32 (8082 hom., cov: 32)
• Consequence: ENSG00000302625 ENST00000788220.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 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=-0.77).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.361 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

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000302625	ENST00000788220.1		n.124+689C>T		intron	N/A
	ENSG00000302625	ENST00000788221.1		n.486+297C>T		intron	N/A
	ENSG00000302625	ENST00000788222.1		n.478+43C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.320 AC: 48568 AN: 151908 Hom.: 8079 Cov.: 32

Gnomad AFR AF: 0.286

Gnomad AMI AF: 0.200

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.276

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.410

Gnomad MID AF: 0.275

Gnomad NFE AF: 0.365

Gnomad OTH AF: 0.286

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

GnomAD4 genome AF: 0.320 AC: 48612 AN: 152026 Hom.: 8082 Cov.: 32 AF XY: 0.319 AC XY: 23670 AN XY: 74294

African (AFR) AF: 0.287 AC: 11877 AN: 41446

American (AMR) AF: 0.205 AC: 3129 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 910 AN: 3470

East Asian (EAS) AF: 0.275 AC: 1427 AN: 5180

South Asian (SAS) AF: 0.265 AC: 1272 AN: 4806

European-Finnish (FIN) AF: 0.410 AC: 4330 AN: 10550

Middle Eastern (MID) AF: 0.279 AC: 82 AN: 294

European-Non Finnish (NFE) AF: 0.365 AC: 24802 AN: 67968

Other (OTH) AF: 0.285 AC: 601 AN: 2110

Alfa AF: 0.343 Hom.: 1363

Bravo AF: 0.301

Asia WGS AF: 0.244 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.77
CADD	Benign	6.1
DANN	Benign	0.89
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs6976843; hg19: chr7-33103303;