rs3802910

Variant names:

• chr11-121902047-G-A
• rs3802910
• ENST00000652518.1:n.355-4260G>A

Variant summary

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

The ENST00000652518.1(ENSG00000286044):​n.355-4260G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0362 in 152,144 control chromosomes in the GnomAD database, including 218 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 0.036 (218 hom., cov: 32)
• Consequence: ENSG00000286044 ENST00000652518.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325
• Publications: 1 publications found

Genes affected

ENSG00000286044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652518.1. 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
	ENSG00000286044	ENST00000652518.1		n.355-4260G>A		intron	N/A
	ENSG00000286044	ENST00000652677.1		n.616-2343G>A		intron	N/A
	ENSG00000286044	ENST00000746940.1		n.532-4260G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0361 AC: 5491 AN: 152026 Hom.: 212 Cov.: 32

Gnomad AFR AF: 0.0138

Gnomad AMI AF: 0.0296

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.0210

Gnomad EAS AF: 0.135

Gnomad SAS AF: 0.0312

Gnomad FIN AF: 0.0220

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0289

Gnomad OTH AF: 0.0302

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

GnomAD4 genome AF: 0.0362 AC: 5515 AN: 152144 Hom.: 218 Cov.: 32 AF XY: 0.0381 AC XY: 2831 AN XY: 74366

African (AFR) AF: 0.0138 AC: 574 AN: 41506

American (AMR) AF: 0.112 AC: 1705 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0210 AC: 73 AN: 3472

East Asian (EAS) AF: 0.136 AC: 704 AN: 5182

South Asian (SAS) AF: 0.0314 AC: 151 AN: 4806

European-Finnish (FIN) AF: 0.0220 AC: 233 AN: 10586

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0290 AC: 1969 AN: 68010

Other (OTH) AF: 0.0351 AC: 74 AN: 2108

Alfa AF: 0.0309 Hom.: 10

Bravo AF: 0.0448

Asia WGS AF: 0.0720 AC: 248 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	2.1
DANN	Benign	0.57
PhyloP100		-0.33

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: rs3802910;

hg19: chr11-121772755;