rs7243404

Variant names:

• chr18-77192881-T-G
• rs7243404
• ENST00000584843.1:n.209+7584T>G

Variant summary

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

The ENST00000584843.1(ENSG00000265844):​n.209+7584T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.227 in 152,066 control chromosomes in the GnomAD database, including 3,983 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 0.23 (3983 hom., cov: 32)
• Consequence: ENSG00000265844 ENST00000584843.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.922
• Publications: 2 publications found

Genes affected

ENSG00000265844 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.23 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
ENSG00000265844	ENST00000584843.1	n.209+7584T>G		intron_variant	Intron 2 of 4	4
ENSG00000265844	ENST00000843890.1	n.538+4294T>G		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.226 AC: 34403 AN: 151948 Hom.: 3974 Cov.: 32

Gnomad AFR AF: 0.231

Gnomad AMI AF: 0.0680

Gnomad AMR AF: 0.237

Gnomad ASJ AF: 0.190

Gnomad EAS AF: 0.171

Gnomad SAS AF: 0.202

Gnomad FIN AF: 0.288

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.222

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.227 AC: 34448 AN: 152066 Hom.: 3983 Cov.: 32 AF XY: 0.231 AC XY: 17176 AN XY: 74350

African (AFR) AF: 0.231 AC: 9574 AN: 41470

American (AMR) AF: 0.236 AC: 3617 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.190 AC: 659 AN: 3466

East Asian (EAS) AF: 0.171 AC: 881 AN: 5160

South Asian (SAS) AF: 0.204 AC: 985 AN: 4822

European-Finnish (FIN) AF: 0.288 AC: 3043 AN: 10576

Middle Eastern (MID) AF: 0.216 AC: 63 AN: 292

European-Non Finnish (NFE) AF: 0.222 AC: 15063 AN: 67968

Other (OTH) AF: 0.238 AC: 501 AN: 2104

Alfa AF: 0.216 Hom.: 13680

Bravo AF: 0.220

Asia WGS AF: 0.247 AC: 861 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.9
DANN	Benign	0.84
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs7243404; hg19: chr18-74904837;