chr11-69167951-G-A

Variant names:

• chr11-69167951-G-A
• rs12418451
• ENST00000562772.1:n.477+378C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000562772.1(ENSG00000261070):​n.477+378C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.219 in 151,952 control chromosomes in the GnomAD database, including 4,364 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 0.22 (4364 hom., cov: 31)
• Consequence: ENSG00000261070 ENST00000562772.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.754
• Publications: 54 publications found

Genes affected

ENSG00000261070 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.294 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000562772.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC338694	NR_104161.1		n.475+378C>T		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000261070	ENST00000562772.1	TSL:1	n.477+378C>T		intron	N/A
	ENSG00000306716	ENST00000820373.1		n.154+1043G>A		intron	N/A
	ENSG00000306716	ENST00000820374.1		n.125+1043G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.219 AC: 33283 AN: 151834 Hom.: 4365 Cov.: 31

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.234

Gnomad AMR AF: 0.195

Gnomad ASJ AF: 0.261

Gnomad EAS AF: 0.0383

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.302

Gnomad MID AF: 0.234

Gnomad NFE AF: 0.297

Gnomad OTH AF: 0.257

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

GnomAD4 genome AF: 0.219 AC: 33288 AN: 151952 Hom.: 4364 Cov.: 31 AF XY: 0.217 AC XY: 16102 AN XY: 74256

African (AFR) AF: 0.107 AC: 4444 AN: 41438

American (AMR) AF: 0.194 AC: 2969 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.261 AC: 904 AN: 3470

East Asian (EAS) AF: 0.0382 AC: 197 AN: 5162

South Asian (SAS) AF: 0.123 AC: 592 AN: 4820

European-Finnish (FIN) AF: 0.302 AC: 3190 AN: 10550

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.297 AC: 20177 AN: 67936

Other (OTH) AF: 0.255 AC: 536 AN: 2102

Alfa AF: 0.207 Hom.: 1556

Bravo AF: 0.210

Asia WGS AF: 0.126 AC: 439 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	7.3
DANN	Benign	0.75
PhyloP100		0.75

Splicing

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

Other links and lift over

dbSNP: rs12418451; hg19: chr11-68935419;