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: 18 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000849192.1. 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
	ENSG00000310339	ENST00000849192.1		n.231+21352A>G		intron	N/A

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 v4.9

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs7228085;

hg19: chr18-47160814;