rs7838490

Variant names:

• chr8-88572819-G-A
• rs7838490
• ENST00000518631.1:n.214+29989G>A

Your query was ambiguous. Multiple possible variants found:

• chr8-88572819-G-A
• chr8-88572819-G-T

Variant summary

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

The ENST00000518631.1(ENSG00000253553):​n.214+29989G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.198 in 151,936 control chromosomes in the GnomAD database, including 3,179 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 0.20 (3179 hom., cov: 32)
• Consequence: ENSG00000253553 ENST00000518631.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0120
• Publications: 18 publications found

Genes affected

ENSG00000253553 (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 (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000518631.1. 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
	ENSG00000253553	ENST00000518631.1	TSL:4	n.214+29989G>A		intron	N/A
	ENSG00000253553	ENST00000520312.1	TSL:4	n.156+30060G>A		intron	N/A
	ENSG00000253553	ENST00000521433.1	TSL:4	n.310+30009G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.198 AC: 30061 AN: 151818 Hom.: 3172 Cov.: 32

Gnomad AFR AF: 0.254

Gnomad AMI AF: 0.302

Gnomad AMR AF: 0.159

Gnomad ASJ AF: 0.175

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.218

Gnomad FIN AF: 0.143

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.186

Gnomad OTH AF: 0.206

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

GnomAD4 genome AF: 0.198 AC: 30087 AN: 151936 Hom.: 3179 Cov.: 32 AF XY: 0.197 AC XY: 14616 AN XY: 74232

African (AFR) AF: 0.254 AC: 10523 AN: 41418

American (AMR) AF: 0.159 AC: 2420 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.175 AC: 605 AN: 3466

East Asian (EAS) AF: 0.106 AC: 545 AN: 5150

South Asian (SAS) AF: 0.217 AC: 1044 AN: 4818

European-Finnish (FIN) AF: 0.143 AC: 1509 AN: 10540

Middle Eastern (MID) AF: 0.228 AC: 67 AN: 294

European-Non Finnish (NFE) AF: 0.186 AC: 12672 AN: 67972

Other (OTH) AF: 0.203 AC: 427 AN: 2108

Alfa AF: 0.186 Hom.: 8933

Bravo AF: 0.198

Asia WGS AF: 0.188 AC: 653 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	1.4
DANN	Benign	0.54
PhyloP100		-0.012

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: rs7838490;

hg19: chr8-89585048;