chr11-35063906-T-G

Position:

• chr11-35063906-T-G

Variant summary

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

The ENST00000702237.1(ENSG00000289526):​n.223+2775A>C 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 0.51 in 151,902 control chromosomes in the GnomAD database, including 20,702 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 0.51 (20702 hom., cov: 31)
• Consequence: ENST00000702237.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.618

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105376626	XR_001748180.2	n.705+1214A>C		intron_variant, non_coding_transcript_variant
LOC105376626	XR_007062653.1	n.705+1214A>C		intron_variant, non_coding_transcript_variant
LOC105376626	XR_007062654.1	n.705+1214A>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000702237.1	n.223+2775A>C		intron_variant, non_coding_transcript_variant
	ENST00000685560.1	n.437+1214A>C		intron_variant, non_coding_transcript_variant
	ENST00000701115.1	n.417+1214A>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.510 AC: 77401 AN: 151784 Hom.: 20697 Cov.: 31

Gnomad AFR AF: 0.350

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.600

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.514

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.542

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

GnomAD4 genome AF: 0.510 AC: 77418 AN: 151902 Hom.: 20702 Cov.: 31 AF XY: 0.515 AC XY: 38242 AN XY: 74262

Gnomad4 AFR AF: 0.349

Gnomad4 AMR AF: 0.601

Gnomad4 ASJ AF: 0.610

Gnomad4 EAS AF: 0.753

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.514

Gnomad4 NFE AF: 0.548

Gnomad4 OTH AF: 0.545

Alfa AF: 0.378 Hom.: 1027

Bravo AF: 0.507

Asia WGS AF: 0.685 AC: 2384 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	1.0
DANN	Benign	0.71

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2553772; hg19: chr11-35085453;