11-67362651-A-G

Position:

• chr11-67362651-A-G

Variant summary

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

The ENST00000543494.1(ENSG00000256514):​c.17-9574T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.275 in 152,228 control chromosomes in the GnomAD database, including 11,693 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 0.27 (11693 hom., cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000256514 ENST00000543494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0860

Genes affected

ENSG00000256514 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.697 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
RN7SKP239		n.67362651A>G		intragenic_variant
LOC100130987	NR_024469.1	n.424-24884A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000256514	ENST00000543494.1	c.17-9574T>C		intron_variant		3		ENSP00000480527.1
RN7SKP239	ENST00000364814.1	n.238A>G		non_coding_transcript_exon_variant	1/1	6
RAD9A	ENST00000622583.4	n.392-24884A>G		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41751 AN: 152110 Hom.: 11649 Cov.: 32

Gnomad AFR AF: 0.703

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.312

Gnomad ASJ AF: 0.0559

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.0642

Gnomad FIN AF: 0.110

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.222

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 36 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 16

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.00

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.275 AC: 41858 AN: 152228 Hom.: 11693 Cov.: 32 AF XY: 0.273 AC XY: 20287 AN XY: 74436

Gnomad4 AFR AF: 0.704

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.0559

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.0646

Gnomad4 FIN AF: 0.110

Gnomad4 NFE AF: 0.0657

Gnomad4 OTH AF: 0.221

Alfa AF: 0.106 Hom.: 3284

Bravo AF: 0.315

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	2.5
DANN	Benign	0.44

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs1790740; hg19: chr11-67130122;