chr11-67357752-T-C

Position:

• chr11-67357752-T-C

Variant summary

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

The ENST00000543494.1(ENSG00000256514):​c.17-4675A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,100 control chromosomes in the GnomAD database, including 11,639 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 (11639 hom., cov: 32)
• Consequence: ENSG00000256514 ENST00000543494.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.01

Genes affected

ENSG00000256514 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.696 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC100130987	NR_024469.1	n.424-29783T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000256514	ENST00000543494.1	c.17-4675A>G		intron_variant		3		ENSP00000480527.1
RAD9A	ENST00000622583.4	n.392-29783T>C		intron_variant		2

Frequencies

GnomAD3 genomes AF: 0.274 AC: 41644 AN: 151982 Hom.: 11597 Cov.: 32

Gnomad AFR AF: 0.702

Gnomad AMI AF: 0.0384

Gnomad AMR AF: 0.311

Gnomad ASJ AF: 0.0540

Gnomad EAS AF: 0.233

Gnomad SAS AF: 0.0638

Gnomad FIN AF: 0.109

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.0658

Gnomad OTH AF: 0.222

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

GnomAD4 genome AF: 0.274 AC: 41749 AN: 152100 Hom.: 11639 Cov.: 32 AF XY: 0.272 AC XY: 20225 AN XY: 74368

Gnomad4 AFR AF: 0.703

Gnomad4 AMR AF: 0.311

Gnomad4 ASJ AF: 0.0540

Gnomad4 EAS AF: 0.233

Gnomad4 SAS AF: 0.0642

Gnomad4 FIN AF: 0.109

Gnomad4 NFE AF: 0.0658

Gnomad4 OTH AF: 0.221

Alfa AF: 0.107 Hom.: 3145

Bravo AF: 0.315

Asia WGS AF: 0.221 AC: 767 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	6.7
DANN	Benign	0.84

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: rs1638567; hg19: chr11-67125223;