rs7228085

Variant names:

• chr18-49634444-A-G
• rs7228085
• ENST00000849192.1:n.231+21352A>G

Variant summary

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

The ENST00000849192.1(ENSG00000310339):​n.231+21352A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 152,124 control chromosomes in the GnomAD database, including 22,137 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 0.53 (22137 hom., cov: 33)
• Consequence: ENSG00000310339 ENST00000849192.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 17 publications found

Genes affected

ENSG00000310339 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.659 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105372112	XR_007066363.1	n.178+21575A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000310339	ENST00000849192.1	n.231+21352A>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.530 AC: 80592 AN: 152006 Hom.: 22094 Cov.: 33

Gnomad AFR AF: 0.665

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.434

Gnomad EAS AF: 0.673

Gnomad SAS AF: 0.502

Gnomad FIN AF: 0.488

Gnomad MID AF: 0.547

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.531

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

GnomAD4 genome AF: 0.530 AC: 80694 AN: 152124 Hom.: 22137 Cov.: 33 AF XY: 0.530 AC XY: 39417 AN XY: 74356

African (AFR) AF: 0.665 AC: 27606 AN: 41498

American (AMR) AF: 0.472 AC: 7216 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.434 AC: 1508 AN: 3472

East Asian (EAS) AF: 0.673 AC: 3482 AN: 5176

South Asian (SAS) AF: 0.503 AC: 2426 AN: 4824

European-Finnish (FIN) AF: 0.488 AC: 5153 AN: 10562

Middle Eastern (MID) AF: 0.568 AC: 167 AN: 294

European-Non Finnish (NFE) AF: 0.465 AC: 31629 AN: 67978

Other (OTH) AF: 0.535 AC: 1130 AN: 2112

Alfa AF: 0.498 Hom.: 47151

Bravo AF: 0.537

Asia WGS AF: 0.610 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.67
DANN	Benign	0.49
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs7228085; hg19: chr18-47160814;