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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107984402	XR_007062925.1	n.216-4260G>A		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000286044	ENST00000652518.1	n.355-4260G>A		intron_variant	Intron 3 of 6
ENSG00000286044	ENST00000652677.1	n.616-2343G>A		intron_variant	Intron 5 of 6
ENSG00000286044	ENST00000746940.1	n.532-4260G>A		intron_variant	Intron 3 of 3

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 v4.3

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

Other links and lift over

dbSNP: rs3802910; hg19: chr11-121772755;