rs1374645

Variant names:

• chr11-92940715-C-T
• rs1374645
• ENST00000532770.2:n.146+9709C>T

Variant summary

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

The ENST00000532770.2(ENSG00000254874):​n.146+9709C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0853 in 152,118 control chromosomes in the GnomAD database, including 1,169 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 0.085 (1169 hom., cov: 32)
• Consequence: ENSG00000254874 ENST00000532770.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0660
• Publications: 7 publications found

Genes affected

ENSG00000254874 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.223 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000532770.2. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254874	ENST00000532770.2	TSL:2	n.146+9709C>T		intron	N/A
	ENSG00000254874	ENST00000749785.1		n.128+9709C>T		intron	N/A
	ENSG00000254874	ENST00000749786.1		n.115+9709C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0851 AC: 12933 AN: 152000 Hom.: 1162 Cov.: 32

Gnomad AFR AF: 0.227

Gnomad AMI AF: 0.00220

Gnomad AMR AF: 0.0523

Gnomad ASJ AF: 0.0366

Gnomad EAS AF: 0.00443

Gnomad SAS AF: 0.0648

Gnomad FIN AF: 0.0221

Gnomad MID AF: 0.0854

Gnomad NFE AF: 0.0277

Gnomad OTH AF: 0.0778

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

GnomAD4 genome AF: 0.0853 AC: 12982 AN: 152118 Hom.: 1169 Cov.: 32 AF XY: 0.0841 AC XY: 6255 AN XY: 74384

African (AFR) AF: 0.227 AC: 9416 AN: 41448

American (AMR) AF: 0.0522 AC: 798 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.0366 AC: 127 AN: 3466

East Asian (EAS) AF: 0.00444 AC: 23 AN: 5180

South Asian (SAS) AF: 0.0648 AC: 312 AN: 4814

European-Finnish (FIN) AF: 0.0221 AC: 234 AN: 10596

Middle Eastern (MID) AF: 0.0884 AC: 26 AN: 294

European-Non Finnish (NFE) AF: 0.0277 AC: 1881 AN: 68012

Other (OTH) AF: 0.0770 AC: 163 AN: 2116

Alfa AF: 0.0664 Hom.: 101

Bravo AF: 0.0941

Asia WGS AF: 0.0470 AC: 164 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.4
DANN	Benign	0.78
PhyloP100		0.066

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1374645;

hg19: chr11-92673881;