rs7233060

Variant names:

• chr18-79632379-G-A
• rs7233060
• ENST00000779218.1:n.304+2384C>T

Variant summary

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

The ENST00000779218.1(ENSG00000301485):​n.304+2384C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,164 control chromosomes in the GnomAD database, including 2,426 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 0.17 (2426 hom., cov: 33)
• Consequence: ENSG00000301485 ENST00000779218.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.101
• Publications: 8 publications found

Genes affected

ENSG00000301485 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.239 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000301485	ENST00000779218.1	n.304+2384C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26259 AN: 152048 Hom.: 2415 Cov.: 33

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.0537

Gnomad AMR AF: 0.151

Gnomad ASJ AF: 0.163

Gnomad EAS AF: 0.0545

Gnomad SAS AF: 0.250

Gnomad FIN AF: 0.134

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.163

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.173 AC: 26295 AN: 152164 Hom.: 2426 Cov.: 33 AF XY: 0.170 AC XY: 12615 AN XY: 74396

African (AFR) AF: 0.216 AC: 8960 AN: 41496

American (AMR) AF: 0.151 AC: 2298 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.163 AC: 565 AN: 3470

East Asian (EAS) AF: 0.0548 AC: 284 AN: 5182

South Asian (SAS) AF: 0.251 AC: 1210 AN: 4824

European-Finnish (FIN) AF: 0.134 AC: 1420 AN: 10606

Middle Eastern (MID) AF: 0.163 AC: 48 AN: 294

European-Non Finnish (NFE) AF: 0.163 AC: 11094 AN: 68002

Other (OTH) AF: 0.173 AC: 367 AN: 2116

Alfa AF: 0.168 Hom.: 7881

Bravo AF: 0.174

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	3.4
DANN	Benign	0.42
PhyloP100		0.10

Splicing

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

Other links and lift over

dbSNP: rs7233060; hg19: chr18-77392379; COSMIC: COSV107179526;