rs7581802

Variant names:

• chr2-61862803-A-C
• rs7581802
• ENST00000665043.2:n.336+8302A>C

Your query was ambiguous. Multiple possible variants found:

• chr2-61862803-A-C
• chr2-61862803-A-G

Variant summary

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

The ENST00000665043.2(ENSG00000286360):​n.336+8302A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.183 in 152,140 control chromosomes in the GnomAD database, including 3,126 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 0.18 (3126 hom., cov: 32)
• Consequence: ENSG00000286360 ENST00000665043.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.562
• Publications: 4 publications found

Genes affected

ENSG00000286360 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000665043.2. 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
	ENSG00000286360	ENST00000665043.2		n.336+8302A>C		intron	N/A
	ENSG00000286360	ENST00000761080.1		n.322+8302A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.183 AC: 27804 AN: 152022 Hom.: 3127 Cov.: 32

Gnomad AFR AF: 0.0507

Gnomad AMI AF: 0.162

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.157

Gnomad EAS AF: 0.322

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.280

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.224

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.183 AC: 27811 AN: 152140 Hom.: 3126 Cov.: 32 AF XY: 0.188 AC XY: 13969 AN XY: 74360

African (AFR) AF: 0.0506 AC: 2103 AN: 41548

American (AMR) AF: 0.215 AC: 3279 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.157 AC: 545 AN: 3472

East Asian (EAS) AF: 0.321 AC: 1662 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4822

European-Finnish (FIN) AF: 0.280 AC: 2950 AN: 10548

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.224 AC: 15241 AN: 67984

Other (OTH) AF: 0.200 AC: 422 AN: 2108

Alfa AF: 0.203 Hom.: 11077

Bravo AF: 0.168

Asia WGS AF: 0.324 AC: 1126 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.50
PhyloP100		0.56

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: rs7581802;

hg19: chr2-62089938;