rs1364780

Variant names:

• chr11-127969047-T-C
• rs1364780
• ENST00000823170.1:n.373-16086A>G

Variant summary

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

The ENST00000823170.1(ENSG00000307057):​n.373-16086A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0241 in 152,202 control chromosomes in the GnomAD database, including 138 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 0.024 (138 hom., cov: 32)
• Consequence: ENSG00000307057 ENST00000823170.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.410
• Publications: 4 publications found

Genes affected

ENSG00000307057 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000823170.1. 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
	ENSG00000307057	ENST00000823170.1		n.373-16086A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0241 AC: 3658 AN: 152084 Hom.: 137 Cov.: 32

Gnomad AFR AF: 0.0295

Gnomad AMI AF: 0.00110

Gnomad AMR AF: 0.0287

Gnomad ASJ AF: 0.0314

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.00745

Gnomad FIN AF: 0.0250

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.00888

Gnomad OTH AF: 0.0301

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

GnomAD4 genome AF: 0.0241 AC: 3668 AN: 152202 Hom.: 138 Cov.: 32 AF XY: 0.0252 AC XY: 1877 AN XY: 74428

African (AFR) AF: 0.0300 AC: 1245 AN: 41552

American (AMR) AF: 0.0287 AC: 438 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.0314 AC: 109 AN: 3466

East Asian (EAS) AF: 0.175 AC: 903 AN: 5170

South Asian (SAS) AF: 0.00725 AC: 35 AN: 4830

European-Finnish (FIN) AF: 0.0250 AC: 265 AN: 10614

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.00889 AC: 604 AN: 67972

Other (OTH) AF: 0.0293 AC: 62 AN: 2114

Alfa AF: 0.0137 Hom.: 12

Bravo AF: 0.0271

Asia WGS AF: 0.0850 AC: 294 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	3.5
DANN	Benign	0.56
PhyloP100		0.41

Splicing

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

Other links and lift over

dbSNP: rs1364780; hg19: chr11-127838942;