rs2334659

Positions:

• chr11-1335833-G-A
• chr11-1335833-G-C

Variant summary

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

The ENST00000662307.1(ENSG00000287935):​n.700C>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,132 control chromosomes in the GnomAD database, including 1,123 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 0.11 (1123 hom., cov: 32)
• Consequence: ENSG00000287935 ENST00000662307.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.320

Genes affected

ENSG00000287935 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.8).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC124902606	XR_007062545.1	n.601C>T		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287935	ENST00000662307.1	n.700C>T		non_coding_transcript_exon_variant	3/3

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16209 AN: 152014 Hom.: 1122 Cov.: 32

Gnomad AFR AF: 0.0268

Gnomad AMI AF: 0.118

Gnomad AMR AF: 0.103

Gnomad ASJ AF: 0.131

Gnomad EAS AF: 0.00270

Gnomad SAS AF: 0.0840

Gnomad FIN AF: 0.114

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.162

Gnomad OTH AF: 0.124

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

GnomAD4 genome AF: 0.107 AC: 16210 AN: 152132 Hom.: 1123 Cov.: 32 AF XY: 0.103 AC XY: 7662 AN XY: 74362

Gnomad4 AFR AF: 0.0268

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.131

Gnomad4 EAS AF: 0.00271

Gnomad4 SAS AF: 0.0843

Gnomad4 FIN AF: 0.114

Gnomad4 NFE AF: 0.162

Gnomad4 OTH AF: 0.123

Alfa AF: 0.125 Hom.: 720

Bravo AF: 0.101

Asia WGS AF: 0.0410 AC: 143 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.80
CADD	Benign	1.2
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2334659; hg19: chr11-1357063;