rs7655220

Variant names:

• chr4-22135410-A-G
• rs7655220
• ENST00000510705.3:n.859+33780A>G

Your query was ambiguous. Multiple possible variants found:

• chr4-22135410-A-G
• chr4-22135410-A-T

Variant summary

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

The ENST00000510705.3(ENSG00000250039):​n.859+33780A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.357 in 152,038 control chromosomes in the GnomAD database, including 10,270 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 0.36 (10270 hom., cov: 32)
• Consequence: ENSG00000250039 ENST00000510705.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.296
• Publications: 2 publications found

Genes affected

ENSG00000250039 (HGNC:58742):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.47 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000510705.3. 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
	ENSG00000250039	ENST00000510705.3	TSL:5	n.859+33780A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.357 AC: 54180 AN: 151920 Hom.: 10238 Cov.: 32

Gnomad AFR AF: 0.466

Gnomad AMI AF: 0.319

Gnomad AMR AF: 0.356

Gnomad ASJ AF: 0.226

Gnomad EAS AF: 0.327

Gnomad SAS AF: 0.488

Gnomad FIN AF: 0.296

Gnomad MID AF: 0.312

Gnomad NFE AF: 0.300

Gnomad OTH AF: 0.345

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

GnomAD4 genome AF: 0.357 AC: 54268 AN: 152038 Hom.: 10270 Cov.: 32 AF XY: 0.358 AC XY: 26614 AN XY: 74338

African (AFR) AF: 0.467 AC: 19366 AN: 41486

American (AMR) AF: 0.356 AC: 5430 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.226 AC: 783 AN: 3470

East Asian (EAS) AF: 0.327 AC: 1678 AN: 5138

South Asian (SAS) AF: 0.486 AC: 2345 AN: 4822

European-Finnish (FIN) AF: 0.296 AC: 3131 AN: 10588

Middle Eastern (MID) AF: 0.312 AC: 91 AN: 292

European-Non Finnish (NFE) AF: 0.300 AC: 20411 AN: 67962

Other (OTH) AF: 0.352 AC: 743 AN: 2112

Alfa AF: 0.322 Hom.: 4285

Bravo AF: 0.363

Asia WGS AF: 0.456 AC: 1582 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.9
DANN	Benign	0.62
PhyloP100		-0.30

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: rs7655220;

hg19: chr4-22137033;