11-65481674-A-G

Variant names:

• chr11-65481674-A-G
• rs17146964
• ENST00000776568.1:n.120-13A>G

Variant summary

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

The ENST00000776568.1(ENSG00000301146):​n.120-13A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.178 in 152,090 control chromosomes in the GnomAD database, including 2,566 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 0.18 (2566 hom., cov: 31)
• Consequence: ENSG00000301146 ENST00000776568.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.166
• Publications: 40 publications found

Genes affected

ENSG00000301146 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.193 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000776568.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000301146	ENST00000776568.1		n.120-13A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.178 AC: 27069 AN: 151972 Hom.: 2560 Cov.: 31

Gnomad AFR AF: 0.194

Gnomad AMI AF: 0.297

Gnomad AMR AF: 0.141

Gnomad ASJ AF: 0.188

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.111

Gnomad FIN AF: 0.0839

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.196

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.178 AC: 27092 AN: 152090 Hom.: 2566 Cov.: 31 AF XY: 0.169 AC XY: 12600 AN XY: 74338

African (AFR) AF: 0.194 AC: 8060 AN: 41468

American (AMR) AF: 0.141 AC: 2149 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.188 AC: 651 AN: 3472

East Asian (EAS) AF: 0.155 AC: 800 AN: 5170

South Asian (SAS) AF: 0.112 AC: 539 AN: 4826

European-Finnish (FIN) AF: 0.0839 AC: 890 AN: 10604

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.196 AC: 13308 AN: 67986

Other (OTH) AF: 0.166 AC: 349 AN: 2106

Alfa AF: 0.190 Hom.: 11648

Bravo AF: 0.187

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.7
DANN	Benign	0.71
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs17146964; hg19: chr11-65249145;