rs3802910

Positions:

• chr11-121902047-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000652518.1(ENSG00000286044):​n.355-4260G>A variant causes a intron, non coding transcript 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: ENST00000652518.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.325

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
LOC107984402	XR_007062925.1	n.216-4260G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000652518.1	n.355-4260G>A		intron_variant, non_coding_transcript_variant
	ENST00000652677.1	n.616-2343G>A		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0138

Gnomad4 AMR AF: 0.112

Gnomad4 ASJ AF: 0.0210

Gnomad4 EAS AF: 0.136

Gnomad4 SAS AF: 0.0314

Gnomad4 FIN AF: 0.0220

Gnomad4 NFE AF: 0.0290

Gnomad4 OTH AF: 0.0351

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

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs3802910; hg19: chr11-121772755;